
@article{cock_sanger_2010,
	title = {The Sanger {FASTQ} file format for sequences with quality scores, and the Solexa/Illumina {FASTQ} variants},
	volume = {38},
	rights = {http://creativecommons.org/licenses/by-nc/2.0/uk/},
	issn = {0305-1048, 1362-4962},
	url = {https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkp1137},
	doi = {10.1093/nar/gkp1137},
	pages = {1767--1771},
	number = {6},
	journaltitle = {Nucleic Acids Research},
	author = {Cock, Peter J. A. and Fields, Christopher J. and Goto, Naohisa and Heuer, Michael L. and Rice, Peter M.},
	urldate = {2025-01-30},
	date = {2010-04},
	langid = {english},
}

@article{ni_benchmarking_2023,
	title = {Benchmarking of Nanopore R10.4 and R9.4.1 flow cells in single-cell whole-genome amplification and whole-genome shotgun sequencing},
	volume = {21},
	issn = {20010370},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2001037023001368},
	doi = {10.1016/j.csbj.2023.03.038},
	pages = {2352--2364},
	journaltitle = {Computational and Structural Biotechnology Journal},
	shortjournal = {Computational and Structural Biotechnology Journal},
	author = {Ni, Ying and Liu, Xudong and Simeneh, Zemenu Mengistie and Yang, Mengsu and Li, Runsheng},
	urldate = {2025-01-30},
	date = {2023},
	langid = {english},
}

@article{sanderson_comparison_2023,
	title = {Comparison of R9.4.1/Kit10 and R10/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction},
	volume = {9},
	rights = {http://creativecommons.org/licenses/by/4.0/},
	issn = {2057-5858},
	url = {https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000910},
	doi = {10.1099/mgen.0.000910},
	abstract = {Complete, accurate, cost-effective, and high-throughput reconstruction of bacterial genomes for large-scale genomic epidemiological studies is currently only possible with hybrid assembly, combining long- (typically using nanopore sequencing) and short-read (Illumina) datasets. Being able to use nanopore-only data would be a significant advance. Oxford Nanopore Technologies ({ONT}) have recently released a new flowcell (R10.4) and chemistry (Kit12), which reportedly generate per-read accuracies rivalling those of Illumina data. To evaluate this, we sequenced {DNA} extracts from four commonly studied bacterial pathogens, namely 
               
                 
                  Escherichia coli 
                 
               
              , 
               
                 
                  Klebsiella pneumoniae 
                 
               
              , 
               
                 
                  Pseudomonas aeruginosa 
                 
               
              and 
               
                 
                  Staphylococcus aureus 
                 
               
              , using Illumina and {ONT}’s R9.4.1/Kit10, R10.3/Kit12, R10.4/Kit12 flowcells/chemistries. We compared raw read accuracy and assembly accuracy for each modality, considering the impact of different nanopore basecalling models, commonly used assemblers, sequencing depth, and the use of duplex versus simplex reads. ‘Super accuracy’ (sup) basecalled R10.4 reads - in particular duplex reads - have high per-read accuracies and could be used to robustly reconstruct bacterial genomes without the use of Illumina data. However, the per-run yield of duplex reads generated in our hands with standard sequencing protocols was low (typically {\textless}10 \%), with substantial implications for cost and throughput if relying on nanopore data only to enable bacterial genome reconstruction. In addition, recovery of small plasmids with the best-performing long-read assembler (Flye) was inconsistent. R10.4/Kit12 combined with sup basecalling holds promise as a singular sequencing technology in the reconstruction of commonly studied bacterial genomes, but hybrid assembly (Illumina+R9.4.1 hac) currently remains the highest throughput, most robust, and cost-effective approach to fully reconstruct these bacterial genomes.},
	number = {1},
	journaltitle = {Microbial Genomics},
	author = {Sanderson, Nicholas D. and Kapel, Natalia and Rodger, Gillian and Webster, Hermione and Lipworth, Samuel and Street, Teresa L. and Peto, Timothy and Crook, Derrick and Stoesser, Nicole},
	urldate = {2025-01-30},
	date = {2023-01-10},
	langid = {english},
}

@article{ratcliff_improved_2024,
	title = {Improved resolution of avian influenza virus using Oxford Nanopore R10 sequencing chemistry},
	volume = {12},
	issn = {2165-0497},
	url = {https://journals.asm.org/doi/10.1128/spectrum.01880-24},
	doi = {10.1128/spectrum.01880-24},
	abstract = {{ABSTRACT} 
             
               
               
                Highly pathogenic avian influenza viruses continue to pose global risks to One Health, including agriculture, public, and animal health. Rapid and accurate genomic surveillance is critical for monitoring viral mutations, tracing transmission, and guiding interventions in near real-time. Oxford Nanopore sequencing holds promise for real-time influenza genotyping, but data quality from R9 chemistry has limited its adoption due to challenges resolving low-complexity regions such as the biologically critical hemagglutinin cleavage site, a homopolymer of basic amino acids that distinguish highly pathogenic strains. In this study, human and avian influenza isolates ( 
                n 
                = 45) from Cambodia were sequenced using both R9.4.1 and R10.4.1 flow cells and chemistries to evaluate performance between approaches. Overall, R10.4.1 yielded increased data output with higher average quality compared to R9.4.1, producing improved consensus sequences using a reference-based bioinformatics approach. R10.4.1 had significantly lower minor population insertion and deletion frequencies, driven by improved performance in low sequence complexity regions prone to insertion and deletion errors, such as homopolymers. Within the hemagglutinin cleavage site, R10.4.1 resolved the correct motif in 90\% of genomes compared to only 60\% with R9.4.1. Further examination showed reduced frameshift mutations in consensus sequences generated with R10.4.1 that could result in incorrectly classified virulence with automated pipelines. Improved consensus genome quality from nanopore sequencing approaches, especially across biologically important low-complexity regions, is critical to reduce subjective hand-curation and will improve local and global genomic surveillance responses. 
               
             
             
              {IMPORTANCE} 
              This study demonstrates significant advancement in the field of influenza virus genomic surveillance by showcasing the superior accuracy and data quality of the Oxford Nanopore R10 sequencing chemistry compared to the older R9 chemistry. Improved resolution, including in the critical hemagglutinin multi-basic cleavage site, enables more reliable monitoring and tracking of viral mutations. This accelerates the ability to respond quickly to outbreaks, potentially improving impacts on public health, agriculture, and the economy by enabling more accurate and timely interventions. 
             
          ,  
            This study demonstrates significant advancement in the field of influenza virus genomic surveillance by showcasing the superior accuracy and data quality of the Oxford Nanopore R10 sequencing chemistry compared to the older R9 chemistry. Improved resolution, including in the critical hemagglutinin multi-basic cleavage site, enables more reliable monitoring and tracking of viral mutations. This accelerates the ability to respond quickly to outbreaks, potentially improving impacts on public health, agriculture, and the economy by enabling more accurate and timely interventions.},
	pages = {e01880--24},
	number = {12},
	journaltitle = {Microbiology Spectrum},
	shortjournal = {Microbiol Spectr},
	author = {Ratcliff, Jeremy D. and Merritt, Brian and Gooden, Hannah and Siegers, Jurre Y. and Srikanth, Abhinaya and Yann, Sokhoun and Kol, Sonita and Sin, Sarath and Tok, Songha and Karlsson, Erik A. and Thielen, Peter M.},
	editor = {De Vries, Robert Paul},
	urldate = {2025-01-30},
	date = {2024-12-05},
	langid = {english},
}

@article{wongsurawat_native_2022,
	title = {Native {RNA} or {cDNA} Sequencing for Transcriptomic Analysis: A Case Study on Saccharomyces cerevisiae},
	volume = {10},
	issn = {2296-4185},
	url = {https://www.frontiersin.org/articles/10.3389/fbioe.2022.842299/full},
	doi = {10.3389/fbioe.2022.842299},
	shorttitle = {Native {RNA} or {cDNA} Sequencing for Transcriptomic Analysis},
	abstract = {Direct sequencing of single molecules through nanopores allows for accurate quantification and full-length characterization of native {RNA} or complementary {DNA} ({cDNA}) without amplification. Both nanopore-based native {RNA} and {cDNA} approaches involve complex transcriptome procedures at a lower cost. However, there are several differences between the two approaches. In this study, we perform matched native {RNA} sequencing and {cDNA} sequencing to enable relevant comparisons and evaluation. Using 
              Saccharomyces cerevisiae 
              , a eukaryotic model organism widely used in industrial biotechnology, two different growing conditions are considered for comparison, including the poly-A messenger {RNA} isolated from yeast cells grown in minimum media under respirofermentative conditions supplemented with glucose (glucose growth conditions) and from cells that had shifted to ethanol as a carbon source (ethanol growth conditions). Library preparation for direct {RNA} sequencing is shorter than that for direct {cDNA} sequencing. The sequence characteristics of the two methods were different, such as sequence yields, quality score of reads, read length distribution, and mapped on reference ability of reads. However, differential gene expression analyses derived from the two approaches are comparable. The unique feature of direct {RNA} sequencing is {RNA} modification; we found that the {RNA} modification at the 5′ end of a transcript was underestimated due to the 3′ bias behavior of the direct {RNA} sequencing. Our comprehensive evaluation from this work could help researchers make informed choices when selecting an appropriate long-read sequencing method for understanding gene functions, pathways, and detailed functional characterization.},
	pages = {842299},
	journaltitle = {Frontiers in Bioengineering and Biotechnology},
	shortjournal = {Front. Bioeng. Biotechnol.},
	author = {Wongsurawat, Thidathip and Jenjaroenpun, Piroon and Wanchai, Visanu and Nookaew, Intawat},
	urldate = {2025-01-30},
	date = {2022-04-12},
}

@misc{the_sambam_format_specification_working_group_sequence_2024,
	title = {Sequence Alignment/Map Format Specification},
	url = {http://samtools.github.io/hts-specs/SAMv1.pdf},
	author = {{The SAM/BAM Format Specification Working Group}},
	date = {2024-11-06},
}

@book{mount_bioinformatics_2001,
	location = {Cold Spring Harbor, N.Y},
	title = {Bioinformatics: sequence and genome analysis},
	isbn = {9780879696559 9780879695972 9780879696085},
	shorttitle = {Bioinformatics},
	pagetotal = {564},
	publisher = {Cold Spring Harbor Laboratory Press},
	author = {Mount, David W.},
	date = {2001},
	keywords = {Amino acid sequence, Bioinformatics, Data processing, Genetics, Nucleotide sequence},
}

@online{the_hdf_group_hdf5_2024,
	title = {{HDF}5 Documentation},
	url = {https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_5/documentation/doxygen/},
	author = {{The HDF Group}},
	urldate = {2025-01-30},
	date = {2024},
}

@article{david_nanocall_2017,
	title = {Nanocall: an open source basecaller for Oxford Nanopore sequencing data},
	volume = {33},
	rights = {http://creativecommons.org/licenses/by/4.0/},
	issn = {1367-4803, 1367-4811},
	url = {https://academic.oup.com/bioinformatics/article/33/1/49/2525680},
	doi = {10.1093/bioinformatics/btw569},
	shorttitle = {Nanocall},
	abstract = {Abstract 
             
              Motivation 
              The highly portable Oxford Nanopore {MinION} sequencer has enabled new applications of genome sequencing directly in the field. However, the {MinION} currently relies on a cloud computing platform, Metrichor (metrichor.com), for translating locally generated sequencing data into basecalls. 
             
             
              Results 
              To allow offline and private analysis of {MinION} data, we created Nanocall. Nanocall is the first freely available, open-source basecaller for Oxford Nanopore sequencing data and does not require an internet connection. Using R7.3 chemistry, on two E.coli and two human samples, with natural as well as {PCR}-amplified {DNA}, Nanocall reads have ∼68\% identity, directly comparable to Metrichor ‘1D’ data. Further, Nanocall is efficient, processing ∼2500 Kbp of sequence per core hour using the fastest settings, and fully parallelized. Using a 4 core desktop computer, Nanocall could basecall a {MinION} sequencing run in real time. Metrichor provides the ability to integrate the ‘1D’ sequencing of template and complement strands of a single {DNA} molecule, and create a ‘2D’ read. Nanocall does not currently integrate this technology, and addition of this capability will be an important future development. In summary, Nanocall is the first open-source, freely available, off-line basecaller for Oxford Nanopore sequencing data. 
             
             
              Availability and Implementation 
              Nanocall is available at github.com/mateidavid/nanocall, released under the {MIT} license. 
             
             
              Supplementary information 
              Supplementary data are available at Bioinformatics online.},
	pages = {49--55},
	number = {1},
	journaltitle = {Bioinformatics},
	author = {David, Matei and Dursi, L J and Yao, Delia and Boutros, Paul C and Simpson, Jared T},
	editor = {Birol, Inanc},
	urldate = {2025-01-29},
	date = {2017-01-01},
	langid = {english},
}

@online{oxford_nanopore_technologies_dorado_2025,
	title = {Dorado 0.9.1 Documentation},
	url = {https://dorado-docs.readthedocs.io/en/0.9.1/},
	author = {{Oxford Nanopore Technologies}},
	urldate = {2025-01-26},
	date = {2025},
}

@online{oxford_nanopore_technologies_minion_2017,
	title = {{MinION} and flow cells},
	url = {https://nanoporetech.com/document/hardware},
	abstract = {For Research Use Only},
	titleaddon = {Oxford Nanopore Technologies},
	author = {{Oxford Nanopore Technologies}},
	urldate = {2025-01-25},
	date = {2017-04-16},
	langid = {british},
}

@article{mostafa_evolution_2024,
	title = {An evolution of Nanopore next-generation sequencing technology: implications for medical microbiology and public health},
	volume = {62},
	issn = {0095-1137, 1098-660X},
	url = {https://journals.asm.org/doi/10.1128/jcm.00246-24},
	doi = {10.1128/jcm.00246-24},
	shorttitle = {An evolution of Nanopore next-generation sequencing technology},
	abstract = {{ABSTRACT} 
             
               
               
                Next-generation sequencing has evolved as a powerful tool, with applications that extend from diagnosis to public health surveillance and outbreak investigations. Short-read sequencing, using primarily Illumina chemistry, has been the prevailing approach. Single-molecule sensing and long-read sequencing using Oxford Nanopore Technologies ({ONT}) has witnessed a breakthrough in the evolution of the technology, performance, and applications in the past few years. In this issue of the 
                Journal of Clinical Microbiology 
                , Bogaerts et al. ( 
                https://doi.org/10.1128/jcm.01576-23 
                ) describe the utility of the latest {ONT} sequencing technology, the R10.4.1, in bacterial outbreak investigations. The authors demonstrate that {ONT} R10.4.1 technology can be comparable to Illumina sequencing for single-nucleotide polymorphism-based phylogeny. The authors emphasize that the reproducibility between {ONT} and Illumina technologies could facilitate collaborations among laboratories utilizing different sequencing platforms for outbreak investigations.},
	pages = {e00246--24},
	number = {5},
	journaltitle = {Journal of Clinical Microbiology},
	shortjournal = {J Clin Microbiol},
	author = {Mostafa, Heba H.},
	editor = {Rhoads, Daniel D.},
	urldate = {2025-01-25},
	date = {2024-05-08},
	langid = {english},
}

@online{the_apache_software_foundation_apache_nodate,
	title = {Apache Arrow},
	url = {https://arrow.apache.org/docs/},
	author = {{The Apache Software Foundation}},
	urldate = {2025-01-20},
}

@online{oxford_nanopore_technologies_pod5_2022,
	title = {Pod5 File Format Documentation},
	url = {https://pod5-file-format.readthedocs.io/en/latest/},
	author = {{Oxford Nanopore Technologies}},
	urldate = {2025-01-06},
	date = {2022},
}

@online{oxford_nanopore_technologies_new_2019,
	title = {New ‘R10’ nanopore released into early access},
	url = {https://nanoporetech.com/news/news-new-r10-nanopore-released-early-access},
	abstract = {R10 is a new design of nanopore, with a longer barrel and dual reader head.  This week it is being released from internal use into an early access programme.  A small number of nanopore users will be able to evaluate it and provide feedback, so that Oxford Nanopore can rapidly improve R10},
	titleaddon = {Oxford Nanopore Technologies},
	author = {{Oxford Nanopore Technologies}},
	urldate = {2025-01-06},
	date = {2019-03-13},
	langid = {british},
}

@article{roberts_reducing_2004,
	title = {Reducing storage requirements for biological sequence comparison},
	volume = {20},
	issn = {1367-4811, 1367-4803},
	url = {https://academic.oup.com/bioinformatics/article/20/18/3363/202143},
	doi = {10.1093/bioinformatics/bth408},
	abstract = {Abstract 
            Motivation: Comparison of nucleic acid and protein sequences is a fundamental tool of modern bioinformatics. A dominant method of such string matching is the ‘seed-and-extend’ approach, in which occurrences of short subsequences called ‘seeds’ are used to search for potentially longer matches in a large database of sequences. Each such potential match is then checked to see if it extends beyond the seed. To be effective, the seed-and-extend approach needs to catalogue seeds from virtually every substring in the database of search strings. Projects such as mammalian genome assemblies and large-scale protein matching, however, have such large sequence databases that the resulting list of seeds cannot be stored in {RAM} on a single computer. This significantly slows the matching process. 
            Results: We present a simple and elegant method in which only a small fraction of seeds, called ‘minimizers’, needs to be stored. Using minimizers can speed up string-matching computations by a large factor while missing only a small fraction of the matches found using all seeds.},
	pages = {3363--3369},
	number = {18},
	journaltitle = {Bioinformatics},
	author = {Roberts, Michael and Hayes, Wayne and Hunt, Brian R. and Mount, Stephen M. and Yorke, James A.},
	urldate = {2025-01-06},
	date = {2004-12-12},
	langid = {english},
}

@article{altschul_basic_1990,
	title = {Basic local alignment search tool},
	volume = {215},
	rights = {https://www.elsevier.com/tdm/userlicense/1.0/},
	issn = {00222836},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0022283605803602},
	doi = {10.1016/S0022-2836(05)80360-2},
	pages = {403--410},
	number = {3},
	journaltitle = {Journal of Molecular Biology},
	shortjournal = {Journal of Molecular Biology},
	author = {Altschul, Stephen F. and Gish, Warren and Miller, Webb and Myers, Eugene W. and Lipman, David J.},
	urldate = {2025-01-04},
	date = {1990-10},
	langid = {english},
}

@article{li_minimap2_2018,
	title = {Minimap2: pairwise alignment for nucleotide sequences},
	volume = {34},
	rights = {https://academic.oup.com/journals/pages/open\_access/funder\_policies/chorus/standard\_publication\_model},
	issn = {1367-4803, 1367-4811},
	url = {https://academic.oup.com/bioinformatics/article/34/18/3094/4994778},
	doi = {10.1093/bioinformatics/bty191},
	shorttitle = {Minimap2},
	abstract = {Abstract 
             
              Motivation 
              Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length {mRNA} or {cDNA} reads in high throughput and genomic contigs over 100 Mb in length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms. 
             
             
              Results 
              Minimap2 is a general-purpose alignment program to map {DNA} or long {mRNA} sequences against a large reference database. It works with accurate short reads of ≥100 bp in length, ≥1 kb genomic reads at error rate ∼15\%, full-length noisy Direct {RNA} or {cDNA} reads and assembly contigs or closely related full chromosomes of hundreds of megabases in length. Minimap2 does split-read alignment, employs concave gap cost for long insertions and deletions and introduces new heuristics to reduce spurious alignments. It is 3–4 times as fast as mainstream short-read mappers at comparable accuracy, and is ≥30 times faster than long-read genomic or {cDNA} mappers at higher accuracy, surpassing most aligners specialized in one type of alignment. 
             
             
              Availability and implementation 
              https://github.com/lh3/minimap2 
             
             
              Supplementary information 
              Supplementary data are available at Bioinformatics online.},
	pages = {3094--3100},
	number = {18},
	journaltitle = {Bioinformatics},
	author = {Li, Heng},
	editor = {Birol, Inanc},
	urldate = {2025-01-04},
	date = {2018-09-15},
	langid = {english},
}

@online{oxford_nanopore_technologies_guppy_2018,
	title = {Guppy protocol},
	url = {https://nanoporetech.com/document/Guppy-protocol},
	abstract = {Guppy is a bioinformatics toolkit that enables real-time basecalling and several post-processing features that works on Oxford Nanopore Technologies™ sequencing platforms. 

For Research Use Only

**This is a Legacy product**
This software is no longer supported, and we recommend all customers to upgrade to the latest basecaller, Dorado, which is available in {MinKNOW}.

A Dorado-powered basecall server installed with {MinKNOW} is also available as a package for advanced users. ont-dorado-server is available as a free download from the [Software Downloads](https://community.nanoporetech.com/downloads) page. You can find the changelog.md file containing the documentation file ({DOCUMENTATION}.md) in the root of the archives.

If you require further support for any ongoing critical experiments using a Legacy product, please contact Customer Support via email: support@nanoporetech.com.},
	titleaddon = {Oxford Nanopore Technologies},
	author = {{Oxford Nanopore Technologies}},
	urldate = {2025-01-04},
	date = {2018-11-16},
	langid = {british},
}

@online{oxford_nanopore_technologies_nanoporetechbonito_2024,
	title = {nanoporetech/bonito: A {PyTorch} Basecaller for Oxford Nanopore Reads},
	url = {https://github.com/nanoporetech/bonito},
	shorttitle = {{GitHub} - nanoporetech/bonito},
	abstract = {A {PyTorch} Basecaller for Oxford Nanopore Reads. Contribute to nanoporetech/bonito development by creating an account on {GitHub}.},
	titleaddon = {{GitHub}},
	author = {{Oxford Nanopore Technologies}},
	urldate = {2025-01-01},
	date = {2024-06-04},
	langid = {english},
}

@article{teng_chiron_2018,
	title = {Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning},
	volume = {7},
	rights = {http://creativecommons.org/licenses/by/4.0/},
	issn = {2047-217X},
	url = {https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giy037/4966989},
	doi = {10.1093/gigascience/giy037},
	shorttitle = {Chiron},
	abstract = {Abstract 
            Sequencing by translocating {DNA} fragments through an array of nanopores is a rapidly maturing technology that offers faster and cheaper sequencing than other approaches. However, accurately deciphering the {DNA} sequence from the noisy and complex electrical signal is challenging. Here, we report Chiron, the first deep learning model to achieve end-to-end basecalling and directly translate the raw signal to {DNA} sequence without the error-prone segmentation step. Trained with only a small set of 4,000 reads, we show that our model provides state-of-the-art basecalling accuracy, even on previously unseen species. Chiron achieves basecalling speeds of more than 2,000 bases per second using desktop computer graphics processing units.},
	pages = {giy037},
	number = {5},
	journaltitle = {{GigaScience}},
	author = {Teng, Haotian and Cao, Minh Duc and Hall, Michael B and Duarte, Tania and Wang, Sheng and Coin, Lachlan J M},
	urldate = {2024-12-25},
	date = {2018-05-01},
	langid = {english},
}

@article{boza_deepnano_2017,
	title = {{DeepNano}: Deep recurrent neural networks for base calling in {MinION} nanopore reads},
	volume = {12},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0178751},
	doi = {10.1371/journal.pone.0178751},
	shorttitle = {{DeepNano}},
	pages = {e0178751},
	number = {6},
	journaltitle = {{PLOS} {ONE}},
	shortjournal = {{PLoS} {ONE}},
	author = {Boža, Vladimír and Brejová, Broňa and Vinař, Tomáš},
	editor = {Zhi, Degui},
	urldate = {2024-12-25},
	date = {2017-06-05},
	langid = {english},
}

@book{muller_information_2007,
	location = {New York},
	title = {Information retrieval for music and motion},
	isbn = {9783540740476},
	pagetotal = {313},
	publisher = {Springer},
	author = {Müller, Meinard},
	date = {2007},
	note = {{OCLC}: ocn172976996},
	keywords = {Data processing, Human locomotion, Information storage and retrieval systems, Multimedia systems, Music},
}

@article{liu_dna_2021,
	title = {{DNA} methylation-calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation},
	volume = {22},
	issn = {1474-760X},
	url = {https://doi.org/10.1186/s13059-021-02510-z},
	doi = {10.1186/s13059-021-02510-z},
	shorttitle = {{DNA} methylation-calling tools for Oxford Nanopore sequencing},
	abstract = {Nanopore long-read sequencing technology greatly expands the capacity of long-range, single-molecule {DNA}-modification detection. A growing number of analytical tools have been developed to detect {DNA} methylation from nanopore sequencing reads. Here, we assess the performance of different methylation-calling tools to provide a systematic evaluation to guide researchers performing human epigenome-wide studies.},
	pages = {295},
	number = {1},
	journaltitle = {Genome Biology},
	shortjournal = {Genome Biology},
	author = {Liu, Yang and Rosikiewicz, Wojciech and Pan, Ziwei and Jillette, Nathaniel and Wang, Ping and Taghbalout, Aziz and Foox, Jonathan and Mason, Christopher and Carroll, Martin and Cheng, Albert and Li, Sheng},
	urldate = {2024-12-10},
	date = {2021-10-18},
	keywords = {Base modification, {DNA} methylation, Long-read sequencing, Methylation calling, Nanopore sequencing},
}

@misc{oxford_nanopore_technologies_nanoporetechkmer_models_2024,
	title = {nanoporetech/kmer\_models},
	rights = {{MPL}-2.0},
	url = {https://github.com/nanoporetech/kmer_models},
	abstract = {Predictive kmer models for development use},
	publisher = {Oxford Nanopore Technologies},
	author = {{Oxford Nanopore Technologies}},
	urldate = {2024-12-10},
	date = {2024-12-10},
	note = {original-date: 2016-05-06T10:07:01Z},
}

@online{oxford_nanopore_technologies_megalodon_2019,
	title = {Megalodon Algorithm Details — Megalodon 2.3.3 documentation},
	url = {https://nanoporetech.github.io/megalodon/algorithm_details.html},
	author = {{Oxford Nanopore Technologies}},
	urldate = {2024-12-09},
	date = {2019},
}

@article{gamaarachchi_fast_2022,
	title = {Fast nanopore sequencing data analysis with {SLOW}5},
	volume = {40},
	issn = {1087-0156, 1546-1696},
	url = {https://www.nature.com/articles/s41587-021-01147-4},
	doi = {10.1038/s41587-021-01147-4},
	abstract = {Abstract 
            Nanopore sequencing depends on the {FAST}5 file format, which does not allow efficient parallel analysis. Here we introduce {SLOW}5, an alternative format engineered for efficient parallelization and acceleration of nanopore data analysis. Using the example of {DNA} methylation profiling of a human genome, analysis runtime is reduced from more than two weeks to approximately 10.5 h on a typical high-performance computer. {SLOW}5 is approximately 25\% smaller than {FAST}5 and delivers consistent improvements on different computer architectures.},
	pages = {1026--1029},
	number = {7},
	journaltitle = {Nature Biotechnology},
	shortjournal = {Nat Biotechnol},
	author = {Gamaarachchi, Hasindu and Samarakoon, Hiruna and Jenner, Sasha P. and Ferguson, James M. and Amos, Timothy G. and Hammond, Jillian M. and Saadat, Hassaan and Smith, Martin A. and Parameswaran, Sri and Deveson, Ira W.},
	urldate = {2024-12-08},
	date = {2022-07},
	langid = {english},
}

@article{ni_benchmarking_2023-1,
	title = {Benchmarking of Nanopore R10.4 and R9.4.1 flow cells in single-cell whole-genome amplification and whole-genome shotgun sequencing},
	volume = {21},
	issn = {2001-0370},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10070092/},
	doi = {10.1016/j.csbj.2023.03.038},
	abstract = {Third-generation sequencing can be used in human cancer genomics and epigenomic research. Oxford Nanopore Technologies ({ONT}) recently released R10.4 flow cell, which claimed an improved read accuracy compared to R9.4.1 flow cell. To evaluate the benefits and defects of R10.4 flow cell for cancer cell profiling on {MinION} devices, we used the human non-small-cell lung-carcinoma cell line {HCC}78 to construct libraries for both single-cell whole-genome amplification ({scWGA}) and whole-genome shotgun sequencing. The R10.4 and R9.4.1 reads were benchmarked in terms of read accuracy, variant detection, modification calling, genome recovery rate and compared with the next generation sequencing ({NGS}) reads. The results highlighted that the R10.4 outperforms R9.4.1 reads, achieving a higher modal read accuracy of over 99.1\%, superior variation detection, lower false-discovery rate ({FDR}) in methylation calling, and comparable genome recovery rate. To achieve high yields {scWGA} sequencing in the {ONT} platform as {NGS}, we recommended multiple displacement amplification with a modified T7 endonuclease Ⅰ cutting procedure as a promising method. In addition, we provided a possible solution to filter the likely false positive sites among the whole genome region with R10.4 by using {scWGA} sequencing result as a negative control. Our study is the first benchmark of whole genome single-cell sequencing using {ONT} R10.4 and R9.4.1 {MinION} flow cells by clarifying the capacity of genomic and epigenomic profiling within a single flow cell. A promising method for {scWGA} sequencing together with the methylation calling results can benefit researchers who work on cancer cell genomic and epigenomic profiling using third-generation sequencing., 
          
            ga1},
	pages = {2352--2364},
	journaltitle = {Computational and Structural Biotechnology Journal},
	shortjournal = {Comput Struct Biotechnol J},
	author = {Ni, Ying and Liu, Xudong and Simeneh, Zemenu Mengistie and Yang, Mengsu and Li, Runsheng},
	urldate = {2024-12-08},
	date = {2023-03-24},
	pmid = {37025654},
	pmcid = {PMC10070092},
}

@article{rang_squiggle_2018,
	title = {From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy},
	volume = {19},
	issn = {1474-760X},
	url = {https://doi.org/10.1186/s13059-018-1462-9},
	doi = {10.1186/s13059-018-1462-9},
	shorttitle = {From squiggle to basepair},
	abstract = {Nanopore sequencing is a rapidly maturing technology delivering long reads in real time on a portable instrument at low cost. Not surprisingly, the community has rapidly taken up this new way of sequencing and has used it successfully for a variety of research applications. A major limitation of nanopore sequencing is its high error rate, which despite recent improvements to the nanopore chemistry and computational tools still ranges between 5\% and 15\%. Here, we review computational approaches determining the nanopore sequencing error rate. Furthermore, we outline strategies for translation of raw sequencing data into base calls for detection of base modifications and for obtaining consensus sequences.},
	pages = {90},
	number = {1},
	journaltitle = {Genome Biology},
	shortjournal = {Genome Biology},
	author = {Rang, Franka J. and Kloosterman, Wigard P. and de Ridder, Jeroen},
	urldate = {2024-12-07},
	date = {2018-07-13},
	keywords = {Base-calling Algorithm, Cal Basis, Nanopore Sequencing, Polar Nano, Reading Accuracy},
}

@article{wang_nanopore_2021,
	title = {Nanopore sequencing technology, bioinformatics and applications},
	volume = {39},
	rights = {2021 Springer Nature America, Inc.},
	issn = {1546-1696},
	url = {https://www.nature.com/articles/s41587-021-01108-x},
	doi = {10.1038/s41587-021-01108-x},
	abstract = {Rapid advances in nanopore technologies for sequencing single long {DNA} and {RNA} molecules have led to substantial improvements in accuracy, read length and throughput. These breakthroughs have required extensive development of experimental and bioinformatics methods to fully exploit nanopore long reads for investigations of genomes, transcriptomes, epigenomes and epitranscriptomes. Nanopore sequencing is being applied in genome assembly, full-length transcript detection and base modification detection and in more specialized areas, such as rapid clinical diagnoses and outbreak surveillance. Many opportunities remain for improving data quality and analytical approaches through the development of new nanopores, base-calling methods and experimental protocols tailored to particular applications.},
	pages = {1348--1365},
	number = {11},
	journaltitle = {Nature Biotechnology},
	shortjournal = {Nat Biotechnol},
	author = {Wang, Yunhao and Zhao, Yue and Bollas, Audrey and Wang, Yuru and Au, Kin Fai},
	urldate = {2024-12-07},
	date = {2021-11},
	langid = {english},
	keywords = {Bioinformatics, Genome informatics, Sequencing},
}

@article{mackenzie_introduction_2023,
	title = {An Introduction to Nanopore Sequencing: Past, Present, and Future Considerations},
	volume = {14},
	rights = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2072-666X},
	url = {https://www.mdpi.com/2072-666X/14/2/459},
	doi = {10.3390/mi14020459},
	shorttitle = {An Introduction to Nanopore Sequencing},
	abstract = {There has been significant progress made in the field of nanopore biosensor development and sequencing applications, which address previous limitations that restricted widespread nanopore use. These innovations, paired with the large-scale commercialization of biological nanopore sequencing by Oxford Nanopore Technologies, are making the platforms a mainstay in contemporary research laboratories. Equipped with the ability to provide long- and short read sequencing information, with quick turn-around times and simple sample preparation, nanopore sequencers are rapidly improving our understanding of unsolved genetic, transcriptomic, and epigenetic problems. However, there remain some key obstacles that have yet to be improved. In this review, we provide a general introduction to nanopore sequencing principles, discussing biological and solid-state nanopore developments, obstacles to single-base detection, and library preparation considerations. We present examples of important clinical applications to give perspective on the potential future of nanopore sequencing in the field of molecular diagnostics.},
	pages = {459},
	number = {2},
	journaltitle = {Micromachines},
	author = {{MacKenzie}, Morgan and Argyropoulos, Christos},
	urldate = {2024-12-07},
	date = {2023-02},
	langid = {english},
	keywords = {biosensors, epigenetics, genetics, molecular diagnostics, nanopore sequencing, next-generation sequencing, single-molecule analysis, transcriptomics},
}

@article{boza_precise_2023,
	title = {Precise Nanopore Signal Modeling Improves Unsupervised Single-Molecule Methylation Detection},
	url = {https://www.biorxiv.org/content/10.1101/2023.07.13.548926.abstract},
	pages = {2023--07},
	journaltitle = {{bioRxiv}},
	author = {Boža, Vladimír and Batmendijn, Eduard and Perešíni, Peter and Hodorová, Viktória and Lichancová, Hana and Rabatin, Rastislav and Brejová, Broňa and Nosek, Jozef and Vinař, Tomáš},
	urldate = {2024-12-04},
	date = {2023},
}

@article{wick_performance_2019,
	title = {Performance of neural network basecalling tools for Oxford Nanopore sequencing},
	volume = {20},
	issn = {1474-760X},
	url = {https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1727-y},
	doi = {10.1186/s13059-019-1727-y},
	pages = {129},
	number = {1},
	journaltitle = {Genome Biology},
	shortjournal = {Genome Biol},
	author = {Wick, Ryan R. and Judd, Louise M. and Holt, Kathryn E.},
	urldate = {2024-05-16},
	date = {2019-12},
	langid = {english},
}

@article{sitarcik_warpstr_2023,
	title = {{WarpSTR}: determining tandem repeat lengths using raw nanopore signals},
	volume = {39},
	rights = {https://creativecommons.org/licenses/by/4.0/},
	issn = {1367-4811},
	url = {https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btad388/7199589},
	doi = {10.1093/bioinformatics/btad388},
	shorttitle = {{WarpSTR}},
	abstract = {Abstract 
             
              Motivation 
              Short tandem repeats ({STRs}) are regions of a genome containing many consecutive copies of the same short motif, possibly with small variations. Analysis of {STRs} has many clinical uses but is limited by technology mainly due to {STRs} surpassing the used read length. Nanopore sequencing, as one of long-read sequencing technologies, produces very long reads, thus offering more possibilities to study and analyze {STRs}. Basecalling of nanopore reads is however particularly unreliable in repeating regions, and therefore direct analysis from raw nanopore data is required. 
             
             
              Results 
              Here, we present {WarpSTR}, a novel method for characterizing both simple and complex tandem repeats directly from raw nanopore signals using a finite-state automaton and a search algorithm analogous to dynamic time warping. By applying this approach to determine the lengths of 241 {STRs}, we demonstrate that our approach decreases the mean absolute error of the {STR} length estimate compared to basecalling and {STRique}. 
             
             
              Availability and implementation 
              {WarpSTR} is freely available at https://github.com/fmfi-compbio/warpstr},
	pages = {btad388},
	number = {6},
	journaltitle = {Bioinformatics},
	author = {Sitarčík, Jozef and Vinař, Tomáš and Brejová, Broňa and Krampl, Werner and Budiš, Jaroslav and Radvánszky, Ján and Lucká, Mária},
	editor = {Alkan, Can},
	urldate = {2024-05-11},
	date = {2023-06-01},
	langid = {english},
}

@online{hempel_goldenlayout_nodate,
	title = {{GoldenLayout} - a multi-window {JavaScript} layout manager for Webapps},
	url = {http://golden-layout.com/},
	author = {Hempel, Wolfram},
	urldate = {2021-05-16},
}

@software{shahar603_spacex_2021,
	title = {{SpaceX} Launch Telemetry Data},
	rights = {Unlicense License
        , 
      
    

        Unlicense License},
	url = {https://github.com/shahar603/Telemetry-Data},
	abstract = {A collection of telemetry captured from {SpaceX} Launch Webcasts},
	author = {{shahar603}},
	urldate = {2021-05-16},
	date = {2021-05-04},
	note = {original-date: 2017-10-12T13:28:54Z},
	keywords = {spacex, telemetry},
}

@article{acikmese_lossless_2013,
	title = {Lossless Convexification of Nonconvex Control Bound and Pointing Constraints of the Soft Landing Optimal Control Problem},
	volume = {21},
	issn = {1063-6536, 1558-0865},
	url = {http://ieeexplore.ieee.org/document/6428631/},
	doi = {10.1109/TCST.2012.2237346},
	pages = {2104--2113},
	number = {6},
	journaltitle = {{IEEE} Transactions on Control Systems Technology},
	shortjournal = {{IEEE} Trans. Contr. Syst. Technol.},
	author = {Acikmese, Behcet and Carson, John M. and Blackmore, Lars},
	urldate = {2021-05-16},
	date = {2013-11},
}

@online{ross_spacex_nodate,
	title = {{SpaceX} Falcon 9 Downrange Propulsive Landing (No Boostback)},
	url = {https://zlsadesign.com/infographic/trajectory/spacex-falcon9-booster-dpl-no-boostback/},
	abstract = {This is the approximate trajectory of the
{SpaceX} Falcon 9 booster during a downrange
propulsive landing (i.e. ocean landing) on the
{ASDS}.

Note that this is the trajectory of a booster during a
high-performance mission, and does not include a
boostback burn. The approximate trajectory of a
Falcon 9 landing with a boostback burn can be seen here.},
	author = {Ross, Jon},
	urldate = {2021-05-16},
	langid = {english},
}

@book{zeigler_theory_2018,
	location = {{USA}},
	edition = {3rd},
	title = {Theory of Modeling and Simulation: Discrete Event \&amp; Iterative System Computational Foundations},
	isbn = {9780128133705},
	shorttitle = {Theory of Modeling and Simulation},
	abstract = {Theory of Modeling and Simulation: Discrete Event \& Iterative System Computational Foundations, Third Edition, continues the legacy of this authoritative and complete theoretical work. It is ideal for graduate and {PhD} students and working engineers interested in posing and solving problems using the tools of logico-mathematical modeling and computer simulation. Continuing its emphasis on the integration of discrete event and continuous modeling approaches, the work focuses light on {DEVS} and its potential to support the co-existence and interoperation of multiple formalisms in model components. New sections in this updated edition include discussions on important new extensions to theory, including chapter-length coverage of iterative system specification and {DEVS} and their fundamental importance, closure under coupling for iteratively specified systems, existence, uniqueness, non-deterministic conditions, and temporal progressiveness (legitimacy). Presents a 40\% revised and expanded new edition of this classic book with many important post-2000 extensions to core theory Provides a streamlined introduction to Discrete Event System Specification ({DEVS}) formalism for modeling and simulation Packages all the "need-to-know" information on {DEVS} formalism in one place Expanded to include an online ancillary package, including numerous examples of theory and implementation in {DEVS}-based software, student solutions and instructors manual},
	pagetotal = {692},
	publisher = {Academic Press, Inc.},
	author = {Zeigler, Bernard P. and Muzy, Alexandre and Kofman, Ernesto},
	date = {2018},
}

@book{wang_pid_2020,
	edition = {1},
	title = {{PID} Control System Design and Automatic Tuning using {MATLAB}/Simulink},
	isbn = {9781119469346 9781119469414},
	url = {https://onlinelibrary.wiley.com/doi/book/10.1002/9781119469414},
	publisher = {Wiley},
	author = {Wang, Liuping},
	urldate = {2021-05-12},
	date = {2020-03-02},
	langid = {english},
	doi = {10.1002/9781119469414},
}

@book{nise_control_2015,
	location = {Hoboken, {NJ}},
	edition = {Seventh edition},
	title = {Control Systems Engineering},
	isbn = {9781118170519},
	pagetotal = {919},
	publisher = {Wiley},
	author = {Nise, Norman S.},
	date = {2015},
	keywords = {Automatic control, Systems engineering, Textbooks},
}

@online{noauthor_rotation_nodate,
	title = {Rotation order of quatrotate - {MATLAB} Answers - {MATLAB} Central},
	url = {https://www.mathworks.com/matlabcentral/answers/465053-rotation-order-of-quatrotate},
	urldate = {2021-05-11},
}

@online{hunter_cesium_nodate,
	title = {Cesium Language Guide},
	url = {https://github.com/AnalyticalGraphicsInc/czml-writer/wiki/CZML-Guide},
	abstract = {A library for writing {CZML} content for use with Cesium. - {AnalyticalGraphicsInc}/czml-writer},
	titleaddon = {{GitHub}},
	author = {Hunter, Scott},
	urldate = {2021-05-10},
	langid = {english},
}

@online{cesium_gs_inc_cesiumjs_nodate,
	title = {{CesiumJS}},
	url = {https://cesium.com/platform/cesiumjs/},
	abstract = {{CesiumJS} is an open source {JavaScript} library for creating world-class virtual 3D globes. For more than 10 years, Cesium provides the best-in-class performance, precision, visual quality, and ease of use. Used by developers across industries, from aerospace to smart cities to drones, to create interactive web apps for sharing dynamic geospatial data.},
	titleaddon = {Cesium},
	author = {{Cesium GS, Inc.}},
	urldate = {2021-05-10},
	langid = {american},
}

@inproceedings{marwege_first_2019,
	location = {Madrid, Spanien},
	title = {First Wind Tunnel Data of {CALLISTO} - Reusable {VTVL} Launcher First Stage Demonstrator},
	url = {https://elib.dlr.de/128629/},
	abstract = {In order to make access to space more affordable for both scientific and commercial activities the German Aerospace Center ({DLR}), the Japanese Aerospace Exploration Agency ({JAXA}), and the French National Centre for Space Studies ({CNES}) joined in a trilateral agreement to develop and demonstrate the technologies that will be needed for future reusable launch vehicles. In the joined project {CALLISTO} (Cooperative Action Leading to Launcher Innovation in Stage Toss back Operations) a demonstrator for a reusable vertical take-off, vertical landing rocket, acting as first stage, is developed and built. As long-term objective this project aims at paving the way to develop a rocket that can be reused, and the joint efforts of the three agencies will culminate in a demonstrator that will perform its first flights from the Kourou Space Center in French Guyana.
The aerodynamic and aerothermal behaviour of the {CALLISTO} vehicle are investigated at {DLR}, including its challenging configurations with high angles of attack and subsonic up to supersonic flight regimes. To cross-check the aerodynamic data from {CFD} and for the enhancement of the understanding of the aerodynamic characteristics of the vehicle, experiments were performed in the Trisonic Wind Tunnel ({TMK}) at the {DLR} Department of Supersonic- and Hypersonic Flow Technologies in Cologne for Mach numbers between 0.5 and 2.5.
The experiments considered the ascent and the backwards orientated decent configurations of the vehicle with folded and deployed control surfaces at several deflection angles. The angle of attack was continuously varied for all configurations. A comparison between the Aerodynamic Data Base ({AEDB}), generated previously using Euler and Navier-Stokes based {CFD}, and the experimental results showed good agreement and no significant deviations in the global coefficients were found. 
This paper describes the tested configurations and the experimental methods of the test campaign. An uncertainty analysis was performed for the experimental setup and the validity of the data was checked by comparison with other data from preliminary design analysis and {CFD} simulations. Follow-up investigations in {CALLISTO} project will evaluate the influence of the exhaust plume on the aerodynamics of the vehicle which is not covered by the present study.},
	eventtitle = {{EUCASS} 2019},
	author = {Marwege, Ansgar and Riehmer, Johannes and Klevanski, Josef and Gülhan, Ali and Ecker, Tobias and Reimann, Bodo and Dumont, Etienne},
	urldate = {2021-05-08},
	date = {2019-07},
	langid = {english},
}

@inproceedings{dumont_callisto_2018,
	location = {Sevilla, Spanien},
	title = {{CALLISTO} - Reusable {VTVL} launcher first stage demonstrator},
	url = {https://elib.dlr.de/119728/},
	abstract = {{DLR} and {CNES} are jointly developing a demonstrator for a reusable vertical take-off vertical landing launcher first stage. It is called {CALLISTO}, which stands for Cooperative Action Leading to Launcher Innovation in Stage Toss back Operations. The {CALLISTO} project, benefiting from the long heritage and know-how available in Europe is pursuing two main goals. First it shall demonstrate the capabilities to perform the specific manoeuvres and operations needed for an operational reusable first stage performing return to launch site. Second, the repetition of flights will allow confirmation and refinement of the economic assumptions of system studies performed in preparation for the development of a future European launcher.},
	eventtitle = {Space Spropulsion Conference 2018},
	author = {Dumont, Etienne and Ecker, Tobias and Chavagnac, Christophe and Witte, Lars and Windelberg, Jens and Klevanski, Josef and Giagkozoglou, Sofia},
	urldate = {2021-05-08},
	date = {2018-05-15},
	langid = {english},
}

@inproceedings{klevanski_aerodynamic_2018,
	location = {Bremen, Germany},
	title = {Aerodynamic Studies in Preparation for {CALLISTO} - Reusable {VTVL} Launcher First Stage Demonstrator},
	url = {https://elib.dlr.de/122062/},
	abstract = {Reusability applied to launchers is expected to reduce costs of access to space and increase of the operational flexibility. With the goal to improve knowledge in this field, {DLR}, {CNES} and {JAXA} are jointly developing a vertical take-off and landing ({VTVL}) reusable and scaled launcher first stage demonstrator. With this vehicle, called {CALLISTO} (Cooperative Action Leading to Launcher Innovation in Stage Toss-back Operations), {DLR}, {CNES} and {JAXA} want to acquire and demonstrate the capability to recover and reuse a vehicle under conditions representative for an operational launcher first stage. Furthermore, during {CALLISTO} flights, data will be gathered to improve knowledge on the operation of reusable vehicle and therefore help optimizing reusability capabilities of future launch systems.
In order to demonstrate the feasibility of the {CALLISTO} project during the system requirement review ({SRR}) and in preparation of the Preliminary Design Review ({PDR}), extensive aerodynamic analyses have been performed.
The entire {CALLISTO} reference mission is complex and includes many flight phases: ascent, tilt-over manoeuvre, descent and landing. During the flight, the vehicle aerodynamic configuration, the mass, the centre of gravity position and the inertia characteristics change significantly. The flight envelope is characterised by a large range of Mach numbers and dynamic pressures, the angle of attack changes from 0° during ascent to 180° during descent and landing. One of the most important flight phases is the controlled descent through the dense layers of the atmosphere
with aerodynamic control surfaces. Therefore aerodynamic design of the vehicle and especially guarantying stability and controllability are of key importance.
The use of classic engineering aero-prediction methods cannot provide the necessary precision and reliability for the estimation of the aerodynamic coefficients even in very early design phase. Therefore {CFD} methods have to be used even in very early design processes.
For instance, the simulation of the retro-propulsion plume is of particular importance, as it has a major impact on base pressure distribution and aerothermal loads. The paper summarises the main findings of the aerodynamic analysis and show the progress made up to now for {CALLISTO} project.},
	eventtitle = {69th International Astronautical Congress ({IAC})},
	author = {Klevanski, Josef and Ecker, Tobias and Riehmer, Johannes and Reimann, Bodo and Dumont, Etienne and Chavagnac, Christophe},
	urldate = {2021-05-08},
	date = {2018-10-04},
	langid = {english},
}

@book{sforza_manned_2016,
	location = {Oxford},
	title = {Manned Spacecraft Design Principles},
	isbn = {9780128044254},
	series = {Elsevier aerospace engineering series},
	pagetotal = {625},
	publisher = {Butterworth-Heinemann},
	author = {Sforza, P. M.},
	date = {2016},
	note = {{OCLC}: ocn946603824},
	keywords = {Manned space flight, Systems engineering},
}

@article{pasand_study_2017,
	title = {A study of spacecraft reaction thruster configurations for attitude control system},
	volume = {32},
	issn = {0885-8985},
	url = {http://ieeexplore.ieee.org/document/8039186/},
	doi = {10.1109/MAES.2017.160104},
	pages = {22--39},
	number = {7},
	journaltitle = {{IEEE} Aerospace and Electronic Systems Magazine},
	shortjournal = {{IEEE} Aerosp. Electron. Syst. Mag.},
	author = {Pasand, Milad and Hassani, Ali and Ghorbani, Mehrdad},
	urldate = {2021-05-04},
	date = {2017-07},
}

@unpublished{the_boeing_company_space_1998,
	title = {Space Shuttle Main Engine Orientation},
	url = {http://large.stanford.edu/courses/2011/ph240/nguyen1/docs/SSME_PRESENTATION.pdf},
	author = {{The Boeing Company}},
	date = {1998},
}

@online{rose_quaternions_2015,
	title = {Quaternions},
	url = {http://danceswithcode.net/engineeringnotes/quaternions/quaternions.html},
	author = {Rose, D},
	urldate = {2021-04-05},
	date = {2015},
}

@article{jia_quaternions_2020,
	title = {Quaternions},
	url = {http://web.cs.iastate.edu/~cs577/handouts/quaternion.pdf},
	journaltitle = {Com S 477/577 Notes},
	author = {Jia, Yan-Bin},
	date = {2020},
}

@online{ch_robotics_understanding_nodate,
	title = {Understanding Quaternions},
	url = {http://www.chrobotics.com/library/understanding-quaternions},
	author = {{CH Robotics}},
	urldate = {2021-04-05},
}

@book{tapley_statistical_2004,
	location = {Amsterdam ; Boston},
	title = {Statistical Orbit Determination},
	isbn = {9780126836301},
	pagetotal = {547},
	publisher = {Elsevier Academic Press},
	author = {Tapley, Byron D. and Schutz, Bob E. and Born, George H.},
	date = {2004},
	keywords = {Artificial satellites, Orbital mechanics, Orbits Mathematical models, Space trajectories},
}

@book{the_mathworks_inc_aerospace_2021,
	title = {Aerospace Blockset™ User's Guide},
	url = {https://www.mathworks.com/help/pdf_doc/aeroblks/aeroblks.pdf},
	author = {{The MathWorks, Inc.}},
	date = {2021},
}

@book{de_iaco_veris_fundamental_2021,
	title = {Fundamental Concepts on Liquid-Propellant Rocket Engines},
	isbn = {9783030547042},
	abstract = {The engine of a rocket vehicle is a machine which produces thrust by accelerating a gas flowing through the machine. The reaction to this acceleration is the force which drives the vehicle. The amount of thrust generated depends on the mass flow rate of the gas moving through the engine and on the exit velocity of the gas from the nozzle. The gas flow, the liquid propellants, the combustion process, and the principal components of a rocket engine are discussed here.},
	author = {de Iaco Veris, Alessandro},
	editor = {de Iaco Veris, Alessandro},
	date = {2021},
	doi = {10.1007/978-3-030-54704-2_1},
}

@collection{fortescue_spacecraft_2003,
	location = {New York},
	edition = {3rd ed},
	title = {Spacecraft systems engineering},
	isbn = {9780470851029 9780471619512},
	pagetotal = {678},
	publisher = {J. Wiley},
	editor = {Fortescue, Peter W. and Stark, John and Swinerd, Graham},
	date = {2003},
	keywords = {Astronautics, Design and construction, Space vehicles, Systems engineering},
}

@report{national_aeronautics_and_space_administration_us_1976,
	title = {U.S. Standard Atmosphere},
	url = {https://ntrs.nasa.gov/citations/19770009539},
	number = {{NASA}-{TM}-X-74335},
	author = {{National Aeronautics and Space Administration}},
	date = {1976},
}

@book{stengel_flight_2004,
	location = {Princeton, {NJ}},
	title = {Flight Dynamics},
	isbn = {9780691114071},
	pagetotal = {845},
	publisher = {Princeton University Press},
	author = {Stengel, Robert F.},
	date = {2004},
	keywords = {Aerodynamics, Airplanes, Flight, Performance},
}

@book{saha_earths_2008,
	location = {Berlin},
	title = {The Earth's Atmosphere: Its Physics and Dynamics},
	isbn = {9783540784265},
	shorttitle = {The Earth's Atmosphere},
	pagetotal = {367},
	publisher = {Springer},
	author = {Saha, Kshudiram},
	date = {2008},
	note = {{OCLC}: ocn213114189},
	keywords = {Atmospheric physics, Dynamic meteorology},
}

@book{jamshed_using_2015,
	location = {Amsterdam},
	title = {Using {HPC} for computational fluid dynamics: a guide to high performance computing for {CFD} engineers},
	isbn = {9780128015674},
	shorttitle = {Using {HPC} for computational fluid dynamics},
	pagetotal = {213},
	publisher = {Elsevier/Academic Press},
	author = {Jamshed, Shamoon},
	date = {2015},
	note = {{OCLC}: ocn918792203},
	keywords = {Computational fluid dynamics, High performance computing},
}

@book{versteeg_introduction_2007,
	location = {Harlow, England ; New York},
	edition = {2nd ed},
	title = {An introduction to computational fluid dynamics: the finite volume method},
	isbn = {9780131274983},
	shorttitle = {An introduction to computational fluid dynamics},
	pagetotal = {503},
	publisher = {Pearson Education Ltd},
	author = {Versteeg, H. K. and Malalasekera, W.},
	date = {2007},
	note = {{OCLC}: ocm76821177},
	keywords = {Computational fluid dynamics, Finite volume method},
}

@online{scott_lift_2004,
	title = {Lift \& Drag vs. Normal \& Axial Force},
	url = {http://www.aerospaceweb.org/question/aerodynamics/q0194.shtml},
	titleaddon = {Aerospaceweb.org},
	author = {Scott, Jeff},
	urldate = {2021-01-18},
	date = {2004},
}

@book{stevens_aircraft_2016,
	location = {Hoboken, N.J},
	edition = {Third edition},
	title = {Aircraft control and simulation: dynamics, controls design, and autonomous systems},
	isbn = {9781118870983},
	shorttitle = {Aircraft control and simulation},
	pagetotal = {749},
	publisher = {John Wiley \& Sons},
	author = {Stevens, Brian L. and Lewis, Frank L. and Johnson, Eric N.},
	date = {2016},
	note = {{OCLC}: ocn935444384},
	keywords = {Airplanes, Control systems},
}

@book{merhav_aerospace_2012,
	location = {New York, {NY}},
	edition = {Softcover repr. of the hardcover 1st ed. 1996},
	title = {Aerospace sensor systems and applications},
	isbn = {9781461284659},
	pagetotal = {454},
	publisher = {Springer},
	author = {Merhav, Shmuel},
	date = {2012},
	note = {{OCLC}: 934917315},
}

@book{groves_principles_2013,
	location = {Boston},
	edition = {2nd ed},
	title = {Principles of {GNSS}, inertial, and multisensor integrated navigation systems},
	isbn = {9781608070053},
	series = {{GNSS} technology and application series},
	pagetotal = {776},
	publisher = {Artech House},
	author = {Groves, Paul D.},
	date = {2013},
	note = {{OCLC}: ocn820530994},
	keywords = {Artificial satellites in navigation, Global Positioning System, Inertial navigation systems, Mobile geographic information systems, Navigation, Technological innovations},
}

@article{blackmore_autonomous_2016,
	title = {Autonomous Precision Landing of Space Rockets},
	volume = {46},
	issn = {0737-6278},
	pages = {15--20},
	number = {4},
	journaltitle = {The Bridge},
	author = {Blackmore, Lars},
	date = {2016},
}

@book{national_aeronautics_and_space_administration_space_1965,
	title = {Space navigation guidance and control},
	volume = {1},
	url = {https://ntrs.nasa.gov/citations/19660019462},
	author = {{National Aeronautics and Space Administration}},
	urldate = {2021-01-08},
	date = {1965},
	keywords = {Apollo},
}

@inproceedings{zanetti_design_2016,
	title = {Design and Flight Performance of the Orion Pre-Launch Navigation System},
	url = {https://ntrs.nasa.gov/citations/20160010463},
	eventtitle = {{AIAA}/{AAS} Astrodynamics Specialist Conference},
	publisher = {{NASA} Johnson Space Center},
	author = {Zanetti, Renato},
	urldate = {2021-01-08},
	date = {2016},
	keywords = {Orion, Sensor models, Sensors},
}

@book{haeussermann_description_1970,
	title = {Description and performance of the Saturn launch vehicle's navigation, guidance, and control system},
	url = {https://ntrs.nasa.gov/citations/19700023342},
	publisher = {{NASA} Marshall Space Flight Center},
	author = {Haeussermann, Walter},
	urldate = {2021-01-08},
	date = {1970},
}

@inproceedings{oliver_space_2018,
	title = {Space Launch Systems Block 1B Preliminary Navigation System Design},
	url = {https://ntrs.nasa.gov/citations/20180002039},
	eventtitle = {Annual American Astronautical Society ({AAS}) Guidance and Control (G\&C) Conference},
	author = {Oliver, T. Emerson and Park, Thomas and Anzalone, Evan and Smith, Austin and Strickland, Dennis and Patrick, Sean},
	urldate = {2021-01-08},
	date = {2018},
}

@book{cai_unmanned_2011,
	location = {New York},
	title = {Unmanned rotorcraft systems},
	isbn = {9780857296344},
	series = {Advances in industrial control},
	pagetotal = {267},
	publisher = {Springer},
	author = {Cai, Guowei and Chen, Ben M. and Lee, Tong Heng},
	date = {2011},
	keywords = {Design and construction, Drone aircraft, Helicopters},
}

@incollection{braun_advances_2013,
	title = {Advances in Inertial Guidance Technology for Aerospace Systems},
	url = {https://arc.aiaa.org/doi/10.2514/6.2013-5123},
	series = {Guidance, Navigation, and Control and Co-located Conferences},
	volumes = {0},
	booktitle = {{AIAA} Guidance, Navigation, and Control ({GNC}) Conference},
	publisher = {American Institute of Aeronautics and Astronautics},
	author = {Braun, Robert D. and Putnam, Zachary R. and Steinfeldt, Bradley A. and Grant, Michael J. and Barton, Gregg},
	urldate = {2020-12-20},
	date = {2013-08-15},
	doi = {10.2514/6.2013-5123},
}

@unpublished{ortega_esa_2014,
	title = {{ESA} Guidance, Navigation and Control Systems},
	url = {http://www.et.tu-dresden.de/ifa/fileadmin/user_upload/www_files/Aktuelles/2014-01-27_ESA_Guidance__Navigation__and_Control_Systems.pdf},
	note = {Dresdner Automatisierungstechnischen Kolloquien},
	author = {Ortega, Guillermo},
	date = {2014},
}

@collection{pisacane_fundamentals_2005,
	location = {Oxford ; New York},
	edition = {2nd ed},
	title = {Fundamentals of space systems},
	isbn = {9780195162059},
	series = {The Johns Hopkins University/Applied Physics Laboratory series in science and engineering},
	pagetotal = {828},
	publisher = {Oxford University Press},
	editor = {Pisacane, Vincent L.},
	date = {2005},
	keywords = {Astronautical instruments, Astronautics, Systems engineering},
}

@collection{davies_standard_2003,
	location = {New York},
	title = {The standard handbook for aeronautical and astronautical engineers},
	isbn = {9780071362290},
	series = {{McGraw}-Hill standard handbooks},
	pagetotal = {1},
	publisher = {{McGraw}-Hill},
	editor = {Davies, Mark},
	date = {2003},
	keywords = {Aerospace engineering, Handbooks, manuals, etc},
}

@book{space_exploration_technologies_corp_falcon_2020,
	title = {Falcon User's Guide},
	url = {https://www.spacex.com/media/Falcon_Users_Guide_082020.pdf},
	author = {{Space Exploration Technologies Corp.}},
	date = {2020},
}

@book{national_aeronautics_and_space_administration_project_1965,
	location = {Washington, D.C.},
	title = {Project Apollo Coordinate System Standards},
	url = {http://www.ibiblio.org/apollo/Documents/19700076120.pdf},
	author = {{National Aeronautics and Space Administration}},
	date = {1965},
	keywords = {Apollo},
}

@book{wie_space_2008,
	location = {Reston, {VA}},
	edition = {2nd ed},
	title = {Space vehicle dynamics and control},
	isbn = {9781563479533},
	series = {{AIAA} education series},
	pagetotal = {950},
	publisher = {American Institute of Aeronautics and Astronautics},
	author = {Wie, Bong},
	date = {2008},
	note = {{OCLC}: ocn232786911},
	keywords = {Control systems, Dynamics, Space vehicles},
}

@online{noauthor_reference_nodate,
	title = {Reference Systems and Frames - Navipedia},
	url = {https://gssc.esa.int/navipedia/index.php/Reference_Systems_and_Frames},
	urldate = {2020-12-18},
	keywords = {Coordinate Systems, {ESA}},
}

@online{noauthor_conventional_nodate,
	title = {Conventional Celestial Reference System - Navipedia},
	url = {https://gssc.esa.int/navipedia/index.php/Conventional_Celestial_Reference_System},
	urldate = {2020-12-18},
	keywords = {Coordinate Systems, {ESA}},
}

@online{the_mathworks_inc_about_2020,
	title = {About Aerospace Coordinate Systems - {MATLAB} \& Simulink},
	url = {https://www.mathworks.com/help/aeroblks/about-aerospace-coordinate-systems.html},
	abstract = {Define coordinate systems to represent aircraft and spacecraft motion.},
	author = {{The MathWorks, Inc.}},
	urldate = {2020-12-14},
	date = {2020},
}

@report{koks_using_2008,
	title = {Using Rotations to Build Aerospace Coordinate Systems},
	url = {https://apps.dtic.mil/docs/citations/ADA484864},
	abstract = {Presented here are the main techniques necessary to understand rotations in three dimensions, for use with global visualisation and aerospace simulations. Relevant techniques can be extremely difficult to find in textbooks, so some useful examples are collected here to highlight these techniques. The three standard aerospace coordinate systems are described and built using rotations. The mathematics of rotations is described, using both matrices and quaternions. The necessary calculations are given for analysing standard scenarios that involve the Global Positioning Satellite system for finding line- of-sight directions on Earth, as well as for visualising the world from a cockpit, and for converting to and from the standard software protocol for distributed interactive simulation environments. Appendices then discuss combining rotations, conversions with a particular type of Euler angle convention, the dangers of confusing Euler angles with incremental rotations for software writers, and finally there is a short discussion of interpolation of rotations in computing.},
	number = {{DSTO}-{TN}-0640},
	institution = {{DEFENCE} {SCIENCE} {AND} {TECHNOLOGY} {ORGANISATION} {SALISBURY} ({AUSTRALIA}) {SYSTEMS} {SCIENCES} {LAB}},
	author = {Koks, Don},
	urldate = {2020-12-14},
	date = {2008-08},
	langid = {english},
}

@online{noauthor_iau_2007,
	title = {{IAU} Nomenclature for Fundamental Astronomy},
	url = {https://syrte.obspm.fr/iauWGnfa/index.html},
	date = {2007},
}

@book{grewal_global_2007,
	location = {Hoboken, N.J},
	edition = {2nd ed},
	title = {Global positioning systems, inertial navigation, and integration},
	isbn = {9780470041901},
	pagetotal = {525},
	publisher = {Wiley-Interscience},
	author = {Grewal, Mohinder S. and Weill, Lawrence R. and Andrews, Angus P.},
	date = {2007},
	note = {{OCLC}: ocm70259027},
	keywords = {Global Positioning System, Inertial navigation, Kalman filtering},
}

@book{noureldin_fundamentals_2013,
	location = {Berlin, Heidelberg},
	title = {Fundamentals of Inertial Navigation, Satellite-based Positioning and their Integration},
	isbn = {9783642304651 9783642304668},
	url = {http://link.springer.com/10.1007/978-3-642-30466-8},
	publisher = {Springer Berlin Heidelberg},
	author = {Noureldin, Aboelmagd and Karamat, Tashfeen B. and Georgy, Jacques},
	urldate = {2020-12-13},
	date = {2013},
	langid = {english},
	doi = {10.1007/978-3-642-30466-8},
}

@book{barrows_dynamics_2020,
	location = {Place of publication not identified},
	title = {Dynamics and simulation of flexible rockets.},
	isbn = {9780128199947},
	publisher = {{ELSEVIER} {ACADEMIC} Press},
	author = {{BARROWS}, {JEB}, {TIMOTHY} M. {ORR}},
	date = {2020},
	note = {{OCLC}: 1138680078},
	keywords = {Advanced, No {PDF}},
}

@book{tewari_atmospheric_2007,
	location = {Boston, Mass},
	title = {Atmospheric and space flight dynamics: modeling and simulation with {MATLAB} and Simulink},
	isbn = {9780817644376},
	series = {Modeling and simulation in science, engineering and technology},
	shorttitle = {Atmospheric and space flight dynamics},
	pagetotal = {556},
	publisher = {Birkhäuser},
	author = {Tewari, Ashish},
	date = {2007},
	keywords = {Aeronautics, Astrodynamics, Space flight},
}

@book{durham_aircraft_2013,
	location = {Chichester, West Sussex},
	title = {Aircraft flight dynamics and control},
	isbn = {9781118646786 9781118646793 9781118646809},
	pagetotal = {1},
	publisher = {John Wiley \& Sons, Inc},
	author = {Durham, Wayne},
	date = {2013},
	keywords = {Aerodynamics, Airplanes, Flight, Flight control, Performance},
}

@book{zipfel_modeling_2007,
	location = {Reston, Va},
	edition = {2nd ed},
	title = {Modeling and simulation of aerospace vehicle dynamics},
	isbn = {9781563478758},
	series = {{AIAA} education series},
	pagetotal = {567},
	publisher = {American Institute of Aeronautics and Astronautics},
	author = {Zipfel, Peter H.},
	date = {2007},
	note = {{OCLC}: ocm78072255},
	keywords = {Aerodynamics, Airplanes, Dynamics Mathematical models, Mathematical models, Mathematics, Space vehicles},
}
