@Article{alok17,
  author       = {Anas Al-Okaily and Badar Almarri and Sultan Al Yami and Chun-Hsi Huang},
  date         = {2017-04-01},
  journaltitle = {Journal of Computational Biology},
  title        = {Toward a Better Compression for {DNA} Sequences Using Huffman Encoding},
  doi          = {10.1089/cmb.2016.0151},
  number       = {4},
  pages        = {280--288},
  volume       = {24},
  publisher    = {Mary Ann Liebert Inc},
}

@Online{bam,
  author  = {The SAM/BAM Format Specification Working Group},
  date    = {2022-08-22},
  title   = {Sequence Alignment/Map Format Specification},
  url     = {https://github.com/samtools/hts-specs},
  urldate = {2022-09-12},
  version = {44b4167},
}

@Article{Cock_2009,
  author       = {Peter J. A. Cock and Christopher J. Fields and Naohisa Goto and Michael L. Heuer and Peter M. Rice},
  date         = {2009-12},
  journaltitle = {Nucleic Acids Research},
  title        = {The Sanger {FASTQ} file format for sequences with quality scores, and the Solexa/Illumina {FASTQ} variants},
  doi          = {10.1093/nar/gkp1137},
  number       = {6},
  pages        = {1767--1771},
  volume       = {38},
  publisher    = {Oxford University Press ({OUP})},
}

@Article{cells,
  author       = {Eva Bianconi and Allison Piovesan and Federica Facchin and Alina Beraudi and Raffaella Casadei and Flavia Frabetti and Lorenza Vitale and Maria Chiara Pelleri and Simone Tassani and Francesco Piva and Soledad Perez-Amodio and Pierluigi Strippoli and Silvia Canaider},
  date         = {2013-07},
  journaltitle = {Annals of Human Biology},
  title        = {An estimation of the number of cells in the human body},
  doi          = {10.3109/03014460.2013.807878},
  number       = {6},
  pages        = {463--471},
  volume       = {40},
  publisher    = {Informa {UK} Limited},
}

@Article{dna_structure,
  author       = {J. D. WATSON and F. H. C. CRICK},
  date         = {1953-04},
  journaltitle = {Nature},
  title        = {Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid},
  doi          = {10.1038/171737a0},
  number       = {4356},
  pages        = {737--738},
  volume       = {171},
  publisher    = {Springer Science and Business Media {LLC}},
}

@Article{iupac,
  author       = {Andrew D. Johnson},
  date         = {2010-03},
  journaltitle = {Bioinformatics},
  title        = {An extended {IUPAC} nomenclature code for polymorphic nucleic acids},
  doi          = {10.1093/bioinformatics/btq098},
  number       = {10},
  pages        = {1386--1389},
  volume       = {26},
  publisher    = {Oxford University Press ({OUP})},
}

@TechReport{rfc1951,
  author    = {L Peter Deutsch},
  date      = {1996-05},
  title     = {{DEFLATE} Compressed Data Format Specification version 1.3},
  doi       = {10.17487/rfc1951},
  url       = {https://www.rfc-editor.org/rfc/rfc1951},
  publisher = {{RFC} Editor},
}

@Article{Shannon_1948,
  author       = {C. E. Shannon},
  date         = {1948-07},
  journaltitle = {Bell System Technical Journal},
  title        = {A Mathematical Theory of Communication},
  doi          = {10.1002/j.1538-7305.1948.tb01338.x},
  number       = {3},
  pages        = {379--423},
  volume       = {27},
  publisher    = {Institute of Electrical and Electronics Engineers ({IEEE})},
}

@Online{ucsc,
  author  = {UCSC - University of California, Santa Cruz},
  date    = {2022-10-28},
  title   = {UCSC Genome Browser},
  url     = {https://genome.ucsc.edu/},
  urldate = {2022-10-28},
}

@Online{ensembl,
  author = {Paul Flicek},
  date   = {2022-10-24},
  title  = {ENSEMBL Project},
  url    = {http://www.ensembl.org/},
}

@Online{ga4gh,
  date  = {2022-10-10},
  title = {Global Alliance for Genomics and Health},
  url   = {https://github.com/samtools/hts-specs.},
}

@Online{bed,
  author = {Sanger Institute, Genome Research Limited},
  date   = {2022-10-20},
  title  = {BED Browser Extensible Data},
  url    = {https://samtools.github.io/hts-specs/BEDv1.pdf},
}

@InProceedings{compr-visual,
  author    = {Sami Khuri and Hsiu-Chin Hsu},
  booktitle = {Proceedings of the 2000 {ACM} symposium on Applied computing - {SAC} {\textquotesingle}00},
  date      = {2000},
  title     = {Tools for visualizing text compression algorithms},
  doi       = {10.1145/335603.335716},
  publisher = {{ACM} Press},
}

@Article{lcqs,
  author       = {Jiabing Fu and Bixin Ke and Shoubin Dong},
  date         = {2020-03},
  journaltitle = {{BMC} Bioinformatics},
  title        = {{LCQS}: an efficient lossless compression tool of quality scores with random access functionality},
  doi          = {10.1186/s12859-020-3428-7},
  number       = {1},
  volume       = {21},
  publisher    = {Springer Science and Business Media {LLC}},
}

@Book{delfs_knebl,
  author    = {Delfs, Hans and Knebl, Helmut},
  date      = {2007},
  title     = {Introduction to Cryptography},
  isbn      = {9783540492436},
  pages     = {368},
  publisher = {Springer},
  subtitle  = {Principles and Applications (Information Security and Cryptography)},
}

@Article{cc14,
  author       = {Kashfia Sailunaz and Mohammed Rokibul Alam Kotwal and Mohammad Nurul Huda},
  date         = {2014-03},
  journaltitle = {International Journal of Computer Applications},
  title        = {Data Compression Considering Text Files},
  doi          = {10.5120/15765-4456},
  number       = {11},
  pages        = {27--32},
  volume       = {90},
  publisher    = {Foundation of Computer Science},
}

@Article{cnet13,
  author       = {Manish RajShivare and Yogendra P. S. Maravi and Sanjeev Sharma},
  date         = {2013-10},
  journaltitle = {International Journal of Computer Applications},
  title        = {Analysis of Header Compression Techniques for Networks: A Review},
  doi          = {10.5120/13856-1701},
  number       = {5},
  pages        = {13--20},
  volume       = {80},
  publisher    = {Foundation of Computer Science},
}

@TechReport{rfcgzip,
  author       = {L. Peter Deutsch and Jean-Loup Gailly and Mark Adler and L. Peter Deutsch and Glenn Randers-Pehrson},
  date         = {1996-05},
  title        = {GZIP file format specification version 4.3},
  number       = {1952},
  type         = {RFC},
  howpublished = {Internet Requests for Comments},
  issn         = {2070-1721},
  month        = {May},
  publisher    = {RFC},
  year         = {1996},
}

@Article{huf52,
  author      = {Huffman, David A.},
  title       = {A Method for the Construction of Minimum-Redundancy Codes},
  number      = {9},
  pages       = {1098-1101},
  volume      = {40},
  added-at    = {2009-01-14T00:43:43.000+0100},
  biburl      = {https://www.bibsonomy.org/bibtex/2585b817b85d7278b868329672ddded96/dret},
  description = {dret'd bibliography},
  interhash   = {d00a180c1c2e7851560c2d51e0fd8f92},
  intrahash   = {585b817b85d7278b868329672ddded96},
  journal     = {Proceedings of the Institute of Radio Engineers},
  keywords    = {imported},
  month       = {September},
  timestamp   = {2009-01-14T00:43:44.000+0100},
  uri         = {http://compression.graphicon.ru/download/articles/huff/huffman_1952_minimum-redundancy-codes.pdf},
  year        = {1952},
}

@Article{moffat20,
  author       = {Alistair Moffat},
  date         = {2020-07},
  journaltitle = {{ACM} Computing Surveys},
  title        = {Huffman Coding},
  doi          = {10.1145/3342555},
  number       = {4},
  pages        = {1--35},
  volume       = {52},
  publisher    = {Association for Computing Machinery ({ACM})},
}

@Article{moffat_arith,
  author       = {Alistair Moffat and Radford M. Neal and Ian H. Witten},
  date         = {1998-07},
  journaltitle = {{ACM} Transactions on Information Systems},
  title        = {Arithmetic coding revisited},
  doi          = {10.1145/290159.290162},
  number       = {3},
  pages        = {256--294},
  volume       = {16},
  publisher    = {Association for Computing Machinery ({ACM})},
}

@Article{ris76,
  author       = {J. J. Rissanen},
  date         = {1976-05},
  journaltitle = {{IBM} Journal of Research and Development},
  title        = {Generalized Kraft Inequality and Arithmetic Coding},
  doi          = {10.1147/rd.203.0198},
  number       = {3},
  pages        = {198--203},
  volume       = {20},
  publisher    = {{IBM}},
}

@Article{ieee-float,
  title   = {IEEE Standard for Floating-Point Arithmetic},
  doi     = {10.1109/IEEESTD.2019.8766229},
  pages   = {1-84},
  journal = {IEEE Std 754-2019 (Revision of IEEE 754-2008)},
  year    = {2019},
}

@Article{big-o,
  author = {Mala, Firdous and Ali, Rouf},
  title  = {The Big-O of Mathematics and Computer Science},
  doi    = {10.26855/jamc.2022.03.001},
  pages  = {1-3},
  volume = {6},
  month  = {01},
  year   = {2022},
}

@Article{sam12,
  author       = {Petr Danecek and James K Bonfield and Jennifer Liddle and John Marshall and Valeriu Ohan and Martin O Pollard and Andrew Whitwham and Thomas Keane and Shane A McCarthy and Robert M Davies and Heng Li},
  date         = {2021-01},
  journaltitle = {{GigaScience}},
  title        = {Twelve years of {SAMtools} and {BCFtools}},
  doi          = {10.1093/gigascience/giab008},
  number       = {2},
  volume       = {10},
  publisher    = {Oxford University Press ({OUP})},
}

@Article{cram-origin,
  author       = {Markus Hsi-Yang Fritz and Rasko Leinonen and Guy Cochrane and Ewan Birney},
  date         = {2011-01},
  journaltitle = {Genome Research},
  title        = {Efficient storage of high throughput {DNA} sequencing data using reference-based compression},
  doi          = {10.1101/gr.114819.110},
  number       = {5},
  pages        = {734--740},
  volume       = {21},
  publisher    = {Cold Spring Harbor Laboratory},
}

@Online{illufastq,
  author = {Illumina},
  date   = {2022-11-17},
  title  = {Illumina FASTq file structure explained},
  url    = {https://support.illumina.com/bulletins/2016/04/fastq-files-explained.html},
}

@TechReport{rfcansi,
  author       = {K. Simonsen and},
  title        = {Character Mnemonics and Character Sets},
  number       = {1345},
  type         = {RFC},
  howpublished = {Internet Requests for Comments},
  issn         = {2070-1721},
  month        = {June},
  year         = {1992},
}

@Article{witten87,
  author       = {Ian H. Witten and Radford M. Neal and John G. Cleary},
  date         = {1987-06},
  journaltitle = {Communications of the {ACM}},
  title        = {Arithmetic coding for data compression},
  doi          = {10.1145/214762.214771},
  issn         = {0001-0782},
  number       = {6},
  pages        = {520–540},
  url          = {https://doi.org/10.1145/214762.214771},
  volume       = {30},
  abstract     = {The state of the art in data compression is arithmetic coding, not the better-known Huffman method. Arithmetic coding gives greater compression, is faster for adaptive models, and clearly separates the model from the channel encoding.},
  address      = {New York, NY, USA},
  issue_date   = {June 1987},
  journal      = {Commun. ACM},
  month        = {jun},
  numpages     = {21},
  publisher    = {Association for Computing Machinery ({ACM})},
  year         = {1987},
}

@InProceedings{geco,
  author    = {Diogo Pratas and Armando J. Pinho and Paulo J. S. G. Ferreira},
  booktitle = {2016 Data Compression Conference ({DCC})},
  date      = {2016-03},
  title     = {Efficient Compression of Genomic Sequences},
  doi       = {10.1109/DCC.2016.60},
  publisher = {{IEEE}},
}

@Article{survey,
  author       = {Morteza Hosseini and Diogo Pratas and Armando Pinho},
  date         = {2016-10},
  journaltitle = {Information},
  title        = {A Survey on Data Compression Methods for Biological Sequences},
  doi          = {10.3390/info7040056},
  number       = {4},
  pages        = {56},
  volume       = {7},
  publisher    = {{MDPI} {AG}},
}

@Article{vertical,
  author       = {Kelvin V. Kredens and Juliano V. Martins and Osmar B. Dordal and Mauri Ferrandin and Roberto H. Herai and Edson E. Scalabrin and Br{\'{a}}ulio C. {\'{A}}vila},
  date         = {2020-05},
  journaltitle = {{PLOS} {ONE}},
  title        = {Vertical lossless genomic data compression tools for assembled genomes: A systematic literature review},
  doi          = {10.1371/journal.pone.0232942},
  editor       = {Rashid Mehmood},
  number       = {5},
  pages        = {e0232942},
  volume       = {15},
  publisher    = {Public Library of Science ({PLoS})},
}

@Online{twobit,
  date   = {2022-09-22},
  editor = {UCSC University of California Sata Cruz},
  title  = {TwoBit File Format},
  url    = {https://genome-source.gi.ucsc.edu/gitlist/kent.git/raw/master/src/inc/twoBit.h},
}

@TechReport{isompeg,
  author      = {{ISO Central Secretary}},
  date        = {2020-10},
  institution = {International Organization for Standardization},
  title       = {MPGE-G},
  language    = {en},
  number      = {ISO/IEC 23092-1:2020},
  type        = {Standard},
  url         = {https://www.iso.org/standard/23092.html},
  year        = {2019},
}

@Article{mpeg,
  author    = {Claudio Albert and Tom Paridaens and Jan Voges and Daniel Naro and Junaid J. Ahmad and Massimo Ravasi and Daniele Renzi and Giorgio Zoia and Paolo Ribeca and Idoia Ochoa and Marco Mattavelli and Jaime Delgado and Mikel Hernaez},
  date      = {2018-09},
  title     = {An introduction to {MPEG}-G, the new {ISO} standard for genomic information representation},
  doi       = {10.1101/426353},
  publisher = {Cold Spring Harbor Laboratory},
}

@Article{haplo,
  author       = {Wai Yee Low and Rick Tearle and Ruijie Liu and Sergey Koren and Arang Rhie and Derek M. Bickhart and Benjamin D. Rosen and Zev N. Kronenberg and Sarah B. Kingan and Elizabeth Tseng and Fran{\c{c}}oise Thibaud-Nissen and Fergal J. Martin and Konstantinos Billis and Jay Ghurye and Alex R. Hastie and Joyce Lee and Andy W. C. Pang and Michael P. Heaton and Adam M. Phillippy and Stefan Hiendleder and Timothy P. L. Smith and John L. Williams},
  date         = {2020-04},
  journaltitle = {Nature Communications},
  title        = {Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle},
  doi          = {10.1038/s41467-020-15848-y},
  number       = {1},
  volume       = {11},
  publisher    = {Springer Science and Business Media {LLC}},
}

@Online{ftp-igsr,
  date  = {2022-11-10},
  title = {IGSR: The International Genome Sample Resource},
  url   = {https://ftp.1000genomes.ebi.ac.uk},
}

@Online{ftp-ncbi,
  date  = {2022-11-01},
  title = {NCBI National Center for Biotechnology Information},
  url   = {https://ftp.ncbi.nlm.nih.gov/genomes/},
}

@Online{ftp-ensembl,
  date  = {2022-10-15},
  title = {ENSEMBL Rapid Release},
  url   = {https://ftp.ensembl.org},
}

@Book{cthreading,
  author    = {Quinn, Michael J.},
  title     = {Parallel Programming in C with MPI and OpenMP},
  isbn      = {0071232656},
  publisher = {McGraw-Hill Education Group},
  year      = {2003},
}

@Online{geco-repo,
  author = {Cobilab},
  date   = {2022-11-19},
  title  = {Repositories for the three versions of GeCo},
  url    = {https://github.com/cobilab},
}

@Article{pet21,
  author    = {Sergey V. Petoukhov},
  date      = {2021-10},
  title     = {Tensor Rules in the Stochastic Organization of Genomes and Genetic Stochastic Resonance in Algebraic Biology},
  doi       = {10.20944/preprints202110.0093.v1},
  publisher = {{MDPI} {AG}},
}

@TechReport{iso-ascii,
  author      = {ISO/IEC JTC 1/SC 2 Coded character sets},
  date        = {1998-04},
  institution = {International Organization for Standardization},
  title       = {Information technology — 8-bit single-byte coded graphic character sets — Part 1: Latin alphabet No. 1},
  type        = {Standard},
  address     = {Geneva, CH},
  key         = {ISO8859-1:1998},
  volume      = {1998},
  year        = {1998},
}

@Book{dict,
  author    = {McIntosh, Colin},
  date      = {2013},
  title     = {Cambridge International Dictionary of English},
  isbn      = {9781107035157},
  pages     = {1856},
  publisher = {Cambridge University Press},
}

@TechReport{rfc-udp,
  author       = {J. Postel},
  date         = {1980-08-28},
  institution  = {RFC Editor},
  title        = {User Datagram Protocol},
  doi          = {10.17487/RFC0768},
  number       = {768},
  pagetotal    = {3},
  url          = {https://www.rfc-editor.org/info/rfc768},
  howpublished = {RFC 768},
  month        = aug,
  publisher    = {RFC Editor},
  series       = {Request for Comments},
  year         = {1980},
}

@TechReport{isoutf,
  author = {ISO},
  title  = {ISO/IEC 10646:2020 UTF},
}

@Article{lz77,
  author  = {Ziv, J. and Lempel, A.},
  title   = {A universal algorithm for sequential data compression},
  doi     = {10.1109/TIT.1977.1055714},
  number  = {3},
  pages   = {337-343},
  volume  = {23},
  journal = {IEEE Transactions on Information Theory},
  year    = {1977},
}

@Online{code-analysis,
  author = {Ryan Dewhurst},
  date   = {2022-11-20},
  editor = {Kirsten S and Nick Bloor and Sarah Baso and James Bowie and Evgeniy Ryzhkov and Iberiam and Ann Campbell and Jonathan Marcil and Christina Schelin and Jie Wang and Fabian and Achim and Dirk Wetter},
  title  = {Static Code Analysis},
  url    = {https://owasp.org/www-community/controls/Static_Code_Analysis},
}

@Online{gpl,
  title = {GNU Public License},
  url   = {http://www.gnu.org/licenses/gpl-3.0.html},
}

@Online{mitlic,
  title = {MIT License},
  url   = {https://spdx.org/licenses/MIT.html},
}

@Comment{jabref-meta: databaseType:biblatex;}
