references.bib

@article{Bankevich2012,
  title     = {SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing},
  volume    = {19},
  issn      = {1557-8666},
  url       = {http://dx.doi.org/10.1089/cmb.2012.0021},
  doi       = {10.1089/cmb.2012.0021},
  number    = {5},
  journal   = {Journal of Computational Biology},
  publisher = {Mary Ann Liebert Inc},
  author    = {Bankevich,  Anton and Nurk,  Sergey and Antipov,  Dmitry and Gurevich,  Alexey A. and Dvorkin,  Mikhail and Kulikov,  Alexander S. and Lesin,  Valery M. and Nikolenko,  Sergey I. and Pham,  Son and Prjibelski,  Andrey D. and Pyshkin,  Alexey V. and Sirotkin,  Alexander V. and Vyahhi,  Nikolay and Tesler,  Glenn and Alekseyev,  Max A. and Pevzner,  Pavel A.},
  year      = {2012},
  month     = may,
  pages     = {455–477}
}

@article{Page2017,
  title     = {Comparison of classical multi-locus sequence typing software for next-generation sequencing data},
  volume    = {3},
  issn      = {2057-5858},
  url       = {http://dx.doi.org/10.1099/mgen.0.000124},
  doi       = {10.1099/mgen.0.000124},
  number    = {8},
  journal   = {Microbial Genomics},
  publisher = {Microbiology Society},
  author    = {Page,  Andrew J. and Alikhan,  Nabil-Fareed and Carleton,  Heather A. and Seemann,  Torsten and Keane,  Jacqueline A. and Katz,  Lee S.},
  year      = {2017},
  month     = jun
}

@article{Cock2009,
  title     = {The Sanger FASTQ file format for sequences with quality scores,  and the Solexa/Illumina FASTQ variants},
  volume    = {38},
  issn      = {1362-4962},
  url       = {http://dx.doi.org/10.1093/nar/gkp1137},
  doi       = {10.1093/nar/gkp1137},
  number    = {6},
  journal   = {Nucleic Acids Research},
  publisher = {Oxford University Press (OUP)},
  author    = {Cock,  Peter J. A. and Fields,  Christopher J. and Goto,  Naohisa and Heuer,  Michael L. and Rice,  Peter M.},
  year      = {2009},
  month     = dec,
  pages     = {1767–1771}
}

@article{SarrazinGendron2024,
  title     = {Improving microbial phylogeny with citizen science within a mass-market video game},
  issn      = {1546-1696},
  url       = {http://dx.doi.org/10.1038/s41587-024-02175-6},
  doi       = {10.1038/s41587-024-02175-6},
  journal   = {Nature Biotechnology},
  publisher = {Springer Science and Business Media LLC},
  author    = {Sarrazin-Gendron,  Roman and Ghasemloo Gheidari,  Parham and Butyaev,  Alexander and Keding,  Timothy and Cai,  Eddie and Zheng,  Jiayue and Mutalova,  Renata and Mounthanyvong,  Julien and Zhu,  Yuxue and Nazarova,  Elena and Drogaris,  Chrisostomos and Erhart,  Kornél and Bélanger,  David and Bouffard,  Michael and Davidson,  Joshua and Falaise,  Mathieu and Fiset,  Vincent and Hebert,  Steven and Hewitt,  Dan and Huot,  Jonathan and Kim,  Seung and Moreau-Genest,  Jonathan and Najjab,  David and Prince,  Steve and Saintélien,  Ludger and Brouillette,  Amélie and Richard,  Gabriel and Pitchford,  Randy and Caisse,  Sébastien and Blanchette,  Mathieu and McDonald,  Daniel and Knight,  Rob and Szantner,  Attila and Waldisp\"{u}hl,  Jér\^ome},
  year      = {2024},
  month     = apr
}

@article{Gruening2018,
  title     = {Bioconda: sustainable and comprehensive software distribution for the life sciences},
  volume    = {15},
  issn      = {1548-7105},
  url       = {http://dx.doi.org/10.1038/s41592-018-0046-7},
  doi       = {10.1038/s41592-018-0046-7},
  number    = {7},
  journal   = {Nature Methods},
  publisher = {Springer Science and Business Media LLC},
  author    = {Gr\"{u}ning,  Bj\"{o}rn and Dale,  Ryan and Sj\"{o}din,  Andreas and Chapman,  Brad A. and Rowe,  Jillian and Tomkins-Tinch,  Christopher H. and Valieris,  Renan and K\"{o}ster,  Johannes},
  year      = {2018},
  month     = jul,
  pages     = {475–476}
}

@article{Da_Veiga_Leprevost2017,
  title     = {{BioContainers}: an open-source and community-driven framework
               for software standardization},
  author    = {da Veiga Leprevost, Felipe and Grüning, Björn A and Alves
               Aflitos, Saulo and Röst, Hannes L and Uszkoreit, Julian and
               Barsnes, Harald and Vaudel, Marc and Moreno, Pablo and Gatto,
               Laurent and Weber, Jonas and Bai, Mingze and Jimenez, Rafael C
               and Sachsenberg, Timo and Pfeuffer, Julianus and Vera Alvarez,
               Roberto and Griss, Johannes and Nesvizhskii, Alexey I and
               Perez-Riverol, Yasset},
  journal   = {Bioinformatics (Oxford, England)},
  publisher = {Oxford University Press (OUP)},
  volume    = 33,
  number    = 16,
  pages     = {2580--2582},
  abstract  = {Abstract Motivation BioContainers (biocontainers.pro) is an
               open-source and community-driven framework which provides
               platform independent executable environments for bioinformatics
               software. BioContainers allows labs of all sizes to easily
               install bioinformatics software, maintain multiple versions of
               the same software and combine tools into powerful analysis
               pipelines. BioContainers is based on popular open-source projects
               Docker and rkt frameworks, that allow software to be installed
               and executed under an isolated and controlled environment. Also,
               it provides infrastructure and basic guidelines to create, manage
               and distribute bioinformatics containers with a special focus on
               omics technologies. These containers can be integrated into more
               comprehensive bioinformatics pipelines and different
               architectures (local desktop, cloud environments or HPC
               clusters). Availability and Implementation The software is freely
               available at github.com/BioContainers/.},
  month     = aug,
  year      = 2017,
  url       = {https://academic.oup.com/bioinformatics/article-pdf/33/16/2580/49041124/bioinformatics_33_16_2580.pdf},
  doi       = {10.1093/bioinformatics/btx192},
  issn      = {1367-4803,1367-4811},
  language  = {en}
}