{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:42:00Z","timestamp":1753875720316,"version":"3.41.2"},"reference-count":73,"publisher":"Oxford University Press (OUP)","issue":"5","funder":[{"name":"National Science and Technology Council of the Taiwanese Government","award":["111-2221-E-038-027"],"award-info":[{"award-number":["111-2221-E-038-027"]}]},{"name":"Seven Bridges Cancer Research Data Commons Cloud Resource"},{"DOI":"10.13039\/501100021671","name":"National Cancer Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100021671","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["HHSN261201400008C","17X146","HHSN261201500003I","75N91019D00024"],"award-info":[{"award-number":["HHSN261201400008C","17X146","HHSN261201500003I","75N91019D00024"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000065","name":"National Institute of Neurological Disorders and Stroke","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000065","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Institutes of Health of Bethesda","award":["NS009443-01"],"award-info":[{"award-number":["NS009443-01"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,9,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Implementing a specific cloud resource to analyze extensive genomic data on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a challenge when resources are limited. To overcome this, we repurposed a cloud platform initially designed for use in research on cancer genomics (https:\/\/cgc.sbgenomics.com) to enable its use in research on SARS-CoV-2 to build Cloud Workflow for Viral and Variant Identification (COWID). COWID is a workflow based on the Common Workflow Language that realizes the full potential of sequencing technology for use in reliable SARS-CoV-2 identification and leverages cloud computing to achieve efficient parallelization. COWID outperformed other contemporary methods for identification by offering scalable identification and reliable variant findings with no false-positive results. COWID typically processed each sample of raw sequencing data within 5\u00a0min at a cost of only US$0.01. The COWID source code is publicly available (https:\/\/github.com\/hendrick0403\/COWID) and can be accessed on any computer with Internet access. COWID is designed to be user-friendly; it can be implemented without prior programming knowledge. Therefore, COWID is a time-efficient tool that can be used during a pandemic.<\/jats:p>","DOI":"10.1093\/bib\/bbad280","type":"journal-article","created":{"date-parts":[[2023,8,10]],"date-time":"2023-08-10T10:21:59Z","timestamp":1691662919000},"source":"Crossref","is-referenced-by-count":1,"title":["COWID: an efficient cloud-based genomics workflow for scalable identification of SARS-COV-2"],"prefix":"10.1093","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7963-4174","authenticated-orcid":false,"given":"Hendrick Gao-Min","family":"Lim","sequence":"first","affiliation":[{"name":"Graduate Institute of Biomedical Informatics , College of Medical Science and Technology, , Taipei , Taiwan 11031"},{"name":"Taipei Medical University , College of Medical Science and Technology, , Taipei , Taiwan 11031"},{"name":"Department of Medical Research, Tzu Chi Hospital Indonesia, Pantai Indah Kapuk, Greater Jakarta , Indonesia 14470"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yang C","family":"Fann","sequence":"additional","affiliation":[{"name":"IT and Bioinformatics Program , Division of Intramural, , Bethesda, Maryland , USA 20892"},{"name":"National Institute of Neurological Disorders and Stroke, National Institutes of Health , Division of Intramural, , Bethesda, Maryland , USA 20892"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5074-7941","authenticated-orcid":false,"given":"Yuan-Chii Gladys","family":"Lee","sequence":"additional","affiliation":[{"name":"Graduate Institute of Biomedical Informatics , College of Medical Science and Technology, , Taipei , Taiwan 11031"},{"name":"Taipei Medical University , College of Medical Science and Technology, , Taipei , Taiwan 11031"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,8,9]]},"reference":[{"key":"2023092216501552100_ref1","doi-asserted-by":"crossref","first-page":"1814","DOI":"10.1056\/NEJMoa1211721","article-title":"Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia","volume":"367","author":"Zaki","year":"2012","journal-title":"N Engl J Med"},{"key":"2023092216501552100_ref2","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1038\/s41586-020-2012-7","article-title":"A pneumonia outbreak associated with a new coronavirus of probable bat origin","volume":"579","author":"Zhou","year":"2020","journal-title":"Nature"},{"key":"2023092216501552100_ref3","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1056\/NEJMoa2001017","article-title":"A novel coronavirus from patients with pneumonia in China, 2019","volume":"382","author":"Zhu","year":"2020","journal-title":"N Engl J Med"},{"key":"2023092216501552100_ref4","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1016\/S1473-3099(20)30120-1","article-title":"An interactive web-based dashboard to track COVID-19 in real time","volume":"20","author":"Dong","year":"2020","journal-title":"Lancet Infect Dis"},{"key":"2023092216501552100_ref5","doi-asserted-by":"crossref","first-page":"m1036","DOI":"10.1136\/bmj.m1036","article-title":"Covid-19: WHO declares pandemic because of \"alarming levels\" of spread, severity, and inaction","volume":"368","author":"Mahase","year":"2020","journal-title":"BMJ"},{"key":"2023092216501552100_ref6","doi-asserted-by":"crossref","first-page":"25","DOI":"10.2807\/1560-7917.ES.2020.25.3.2000045","article-title":"Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR","volume":"25","author":"Corman","year":"2020","journal-title":"Euro Surveill"},{"key":"2023092216501552100_ref7","doi-asserted-by":"crossref","first-page":"1755","DOI":"10.1002\/jmv.25855","article-title":"False negative of RT-PCR and prolonged nucleic acid conversion in COVID-19: rather than recurrence","volume":"92","author":"Xiao","year":"2020","journal-title":"J Med Virol"},{"key":"2023092216501552100_ref8","doi-asserted-by":"crossref","first-page":"274","DOI":"10.1038\/s41587-021-00845-3","article-title":"Could mutations of SARS-CoV-2 suppress diagnostic detection?","volume":"39","author":"Ascoli","year":"2021","journal-title":"Nat Biotechnol"},{"key":"2023092216501552100_ref9","doi-asserted-by":"crossref","first-page":"1135","DOI":"10.1038\/nbt1486","article-title":"Next-generation DNA sequencing","volume":"26","author":"Shendure","year":"2008","journal-title":"Nat Biotechnol"},{"key":"2023092216501552100_ref10","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1038\/nrg.2017.113","article-title":"Cloud computing for genomic data analysis and collaboration","volume":"19","author":"Langmead","year":"2018","journal-title":"Nat Rev Genet"},{"key":"2023092216501552100_ref11","doi-asserted-by":"crossref","DOI":"10.2807\/1560-7917.ES.2017.22.13.30494","article-title":"GISAID: global initiative on sharing all influenza data - from vision to reality","volume":"22","author":"Shu","year":"2017","journal-title":"Euro Surveill"},{"key":"2023092216501552100_ref12","doi-asserted-by":"crossref","first-page":"D161","DOI":"10.1093\/nar\/gkab1135","article-title":"GenBank","volume":"50","author":"Sayers","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2023092216501552100_ref13","doi-asserted-by":"crossref","first-page":"D20","DOI":"10.1093\/nar\/gkab1112","article-title":"Database resources of the national center for biotechnology information","volume":"50","author":"Sayers","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2023092216501552100_ref14","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1038\/s41592-022-01444-z","article-title":"Unlocking capacities of genomics for the COVID-19 response and future pandemics","volume":"19","author":"Knyazev","year":"2022","journal-title":"Nat Methods"},{"key":"2023092216501552100_ref15","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1093\/gigascience\/giaa111","article-title":"IDseq-an open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring","volume":"9","author":"Kalantar","year":"2020","journal-title":"Gigascience"},{"key":"2023092216501552100_ref16","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1038\/s41586-021-04332-2","article-title":"Petabase-scale sequence alignment catalyses viral discovery","volume":"602","author":"Edgar","year":"2022","journal-title":"Nature"},{"key":"2023092216501552100_ref17","doi-asserted-by":"crossref","first-page":"D27","DOI":"10.1093\/nar\/gkab951","article-title":"Database resources of the National Genomics Data Center, China National Center for bioinformation in 2022","volume":"50","author":"Members C-N, Partners","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2023092216501552100_ref18","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1016\/j.gpb.2020.09.001","article-title":"The global landscape of SARS-CoV-2 genomes, variants, and haplotypes in 2019nCoVR","volume":"18","author":"Song","year":"2020","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"2023092216501552100_ref19","doi-asserted-by":"crossref","first-page":"D988","DOI":"10.1093\/nar\/gkab1049","article-title":"Ensembl 2022","volume":"50","author":"Cunningham","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2023092216501552100_ref20","doi-asserted-by":"crossref","first-page":"D11","DOI":"10.1093\/nar\/gkab1127","article-title":"The European bioinformatics institute (EMBL-EBI) in 2021","volume":"50","author":"Cantelli","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2023092216501552100_ref21","doi-asserted-by":"crossref","first-page":"D765","DOI":"10.1093\/nar\/gkab889","article-title":"The Ensembl COVID-19 resource: ongoing integration of public SARS-CoV-2 data","volume":"50","author":"De Silva","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2023092216501552100_ref22","doi-asserted-by":"crossref","first-page":"e3","DOI":"10.1158\/0008-5472.CAN-17-0387","article-title":"The cancer genomics cloud: collaborative, reproducible, and democratized-a new paradigm in large-scale computational research","volume":"77","author":"Lau","year":"2017","journal-title":"Cancer Res"},{"key":"2023092216501552100_ref23","doi-asserted-by":"crossref","first-page":"e1006144","DOI":"10.1371\/journal.pcbi.1006144","article-title":"Cloud computing applications for biomedical science: a perspective","volume":"14","author":"Navale","year":"2018","journal-title":"PLoS Comput Biol"},{"key":"2023092216501552100_ref24","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1038\/ng.2764","article-title":"The cancer genome atlas pan-cancer analysis project","volume":"45","author":"Cancer Genome Atlas Research N","year":"2013","journal-title":"Nat Genet"},{"key":"2023092216501552100_ref25","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1016\/j.cell.2018.03.039","article-title":"Pathogenic germline variants in 10,389 adult cancers","volume":"173","author":"Huang","year":"2018","journal-title":"Cell"},{"key":"2023092216501552100_ref26","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1038\/d41573-021-00202-8","article-title":"A tale of two antiviral targets - and the COVID-19 drugs that bind them","volume":"21","author":"Cully","year":"2022","journal-title":"Nat Rev Drug Discov"},{"key":"2023092216501552100_ref27","doi-asserted-by":"crossref","first-page":"705","DOI":"10.24272\/j.issn.2095-8137.2020.065","article-title":"An online coronavirus analysis platform from the National Genomics Data Center","volume":"41","author":"Gong","year":"2020","journal-title":"Zool Res"},{"key":"2023092216501552100_ref28","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1038\/d41586-019-02619-z","article-title":"Workflow systems turn raw data into scientific knowledge","volume":"573","author":"Perkel","year":"2019","journal-title":"Nature"},{"key":"2023092216501552100_ref29","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1007\/978-1-4939-9074-0_24","article-title":"Scalable workflows and reproducible data analysis for genomics","volume":"1910","author":"Strozzi","year":"2019","journal-title":"Methods Mol Biol"},{"key":"2023092216501552100_ref30","first-page":"858","article-title":"Empowering cloud technology for SARS-CoV2 identification","volume":"9","author":"Lim","year":"2020","journal-title":"F1000Research"},{"key":"2023092216501552100_ref31","first-page":"10","article-title":"Orchestrating an optimized next-generation sequencing-based cloud workflow for robust viral identification during pandemics","volume":"10","author":"Lim","year":"2021","journal-title":"Biology (Basel)"},{"key":"2023092216501552100_ref32","doi-asserted-by":"crossref","first-page":"13","DOI":"10.3390\/genes13040686","article-title":"Robust mutation profiling of SARS-CoV-2 variants from multiple raw Illumina sequencing data with cloud workflow","volume":"13","author":"Lim","year":"2022","journal-title":"Genes (Basel)"},{"volume-title":"Figshare","year":"2016","author":"Amstutz","key":"2023092216501552100_ref33"},{"key":"2023092216501552100_ref34","doi-asserted-by":"crossref","first-page":"D57","DOI":"10.1093\/nar\/gkr1163","article-title":"BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata","volume":"40","author":"Barrett","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2023092216501552100_ref35","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1038\/s41392-022-01009-8","article-title":"Omicron: increased transmissibility and decreased pathogenicity","volume":"7","author":"Balint","year":"2022","journal-title":"Signal Transduct Target Ther"},{"key":"2023092216501552100_ref36","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1038\/s41586-022-04411-y","article-title":"Rapid epidemic expansion of the SARS-CoV-2 omicron variant in southern Africa","volume":"603","author":"Viana","year":"2022","journal-title":"Nature"},{"key":"2023092216501552100_ref37","article-title":"Genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans","volume":"3","author":"Boheemen","year":"2012","journal-title":"MBio"},{"key":"2023092216501552100_ref38","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1016\/S0140-6736(20)30251-8","article-title":"Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding","volume":"395","author":"Lu","year":"2020","journal-title":"Lancet"},{"key":"2023092216501552100_ref39","doi-asserted-by":"crossref","first-page":"D387","DOI":"10.1093\/nar\/gkab1053","article-title":"The sequence read archive: a decade more of explosive growth","volume":"50","author":"Katz","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2023092216501552100_ref40","first-page":"154","article-title":"Rabix: an open-source workflow executor supporting Recomputability and interoperability of workflow descriptions","volume":"22","author":"Kaushik","year":"2017","journal-title":"Pac Symp Biocomput"},{"key":"2023092216501552100_ref41","doi-asserted-by":"crossref","first-page":"1721","DOI":"10.1101\/gr.210641.116","article-title":"Centrifuge: rapid and sensitive classification of metagenomic sequences","volume":"26","author":"Kim","year":"2016","journal-title":"Genome Res"},{"key":"2023092216501552100_ref42","doi-asserted-by":"crossref","DOI":"10.1093\/database\/baaa062","article-title":"NCBI taxonomy: a comprehensive update on curation, resources and tools","volume":"2020","author":"Schoch","year":"2020","journal-title":"Database (Oxford)"},{"key":"2023092216501552100_ref43","doi-asserted-by":"crossref","first-page":"D733","DOI":"10.1093\/nar\/gkv1189","article-title":"Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation","volume":"44","author":"O'Leary","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023092216501552100_ref44","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1016\/j.cell.2019.07.010","article-title":"Benchmarking metagenomics tools for taxonomic classification","volume":"178","author":"Ye","year":"2019","journal-title":"Cell"},{"key":"2023092216501552100_ref45","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/ng.806","article-title":"A framework for variation discovery and genotyping using next-generation DNA sequencing data","volume":"43","author":"DePristo","year":"2011","journal-title":"Nat Genet"},{"article-title":"Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM","volume-title":"arXiv preprint","author":"Li","key":"2023092216501552100_ref46"},{"key":"2023092216501552100_ref47","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/1751-0473-9-13","article-title":"Biobambam: tools for read pair collation based algorithms on BAM files","volume":"9","author":"Tischler","year":"2014","journal-title":"Source Code Biol Med"},{"article-title":"Scaling accurate genetic variant discovery to tens of thousands of samples.","year":"2018","author":"Poplin","key":"2023092216501552100_ref48"},{"key":"2023092216501552100_ref49","doi-asserted-by":"crossref","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"Gigascience"},{"key":"2023092216501552100_ref50","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1186\/s13059-021-02490-0","article-title":"STAT: a fast, scalable, MinHash-based k-mer tool to assess sequence read archive next-generation sequence submissions","volume":"22","author":"Katz","year":"2021","journal-title":"Genome Biol"},{"key":"2023092216501552100_ref51","first-page":"213","article-title":"Statistics: a brief overview","volume":"10","author":"Winters","year":"2010","journal-title":"Ochsner J"},{"key":"2023092216501552100_ref52","doi-asserted-by":"crossref","first-page":"veab064","DOI":"10.1093\/ve\/veab064","article-title":"Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool","volume":"7","author":"O'Toole","year":"2021","journal-title":"Virus Evol"},{"key":"2023092216501552100_ref53","doi-asserted-by":"crossref","first-page":"3773","DOI":"10.21105\/joss.03773","article-title":"Nextclade: clade assignment, mutation calling and quality control for viral genomes","volume":"6","author":"Aksamentov","year":"2021","journal-title":"J. Open Source Softw"},{"key":"2023092216501552100_ref54","doi-asserted-by":"crossref","first-page":"991","DOI":"10.1038\/s41588-020-0700-8","article-title":"The UCSC SARS-CoV-2 genome browser","volume":"52","author":"Fernandes","year":"2020","journal-title":"Nat Genet"},{"key":"2023092216501552100_ref55","doi-asserted-by":"crossref","first-page":"D1115","DOI":"10.1093\/nar\/gkab959","article-title":"The UCSC genome browser database: 2022 update","volume":"50","author":"Lee","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2023092216501552100_ref56","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1038\/s41392-022-00992-2","article-title":"Tracking SARS-CoV-2 omicron diverse spike gene mutations identifies multiple inter-variant recombination events","volume":"7","author":"Ou","year":"2022","journal-title":"Signal Transduct Target Ther"},{"key":"2023092216501552100_ref57","doi-asserted-by":"crossref","first-page":"W29","DOI":"10.1093\/nar\/gkt282","article-title":"BLAST: a more efficient report with usability improvements","volume":"41","author":"Boratyn","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023092216501552100_ref58","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1007\/978-0-387-33012-9_1","article-title":"The coronavirus replicase: insights into a sophisticated enzyme machinery","volume":"581","author":"Ziebuhr","year":"2006","journal-title":"Adv Exp Med Biol"},{"key":"2023092216501552100_ref59","doi-asserted-by":"crossref","first-page":"e2200592119","DOI":"10.1073\/pnas.2200592119","article-title":"Omicron mutations enhance infectivity and reduce antibody neutralization of SARS-CoV-2 virus-like particles","volume":"119","author":"Syed","year":"2022","journal-title":"Proc Natl Acad Sci U S A"},{"volume-title":"Guidelines for detecting the SARS-CoV-2 Omicron variant using the Illumina COVIDSeqTM Test (RUO Version)","year":"2022","author":"Illumina","key":"2023092216501552100_ref60"},{"key":"2023092216501552100_ref61","doi-asserted-by":"crossref","first-page":"30679","DOI":"10.1073\/pnas.2007840117","article-title":"Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations","volume":"117","author":"Yang","year":"2020","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2023092216501552100_ref62","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1038\/s41564-022-01089-w","article-title":"Metagenomics-enabled microbial surveillance","volume":"7","author":"Ko","year":"2022","journal-title":"Nat Microbiol"},{"key":"2023092216501552100_ref63","doi-asserted-by":"crossref","first-page":"3903","DOI":"10.1038\/s41467-021-24078-9","article-title":"COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance","volume":"12","author":"Simonetti","year":"2021","journal-title":"Nat Commun"},{"key":"2023092216501552100_ref64","doi-asserted-by":"crossref","first-page":"2520","DOI":"10.1093\/bioinformatics\/bts480","article-title":"Snakemake--a scalable bioinformatics workflow engine","volume":"28","author":"Koster","year":"2012","journal-title":"Bioinformatics"},{"key":"2023092216501552100_ref65","doi-asserted-by":"crossref","first-page":"711437","DOI":"10.3389\/fgene.2021.711437","article-title":"PoreCov-an easy to use, fast, and robust workflow for SARS-CoV-2 genome reconstruction via Nanopore sequencing","volume":"12","author":"Brandt","year":"2021","journal-title":"Front Genet"},{"key":"2023092216501552100_ref66","article-title":"nf-core\/viralrecon: nf-core\/viralrecon v2.5 - Manganese Monkey","volume-title":"Zenodo","author":"Patel","year":"2022"},{"key":"2023092216501552100_ref67","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1038\/nbt.3820","article-title":"Nextflow enables reproducible computational workflows","volume":"35","author":"Di Tommaso","year":"2017","journal-title":"Nat Biotechnol"},{"key":"2023092216501552100_ref68","doi-asserted-by":"crossref","first-page":"5077","DOI":"10.1038\/s41598-022-09035-w","article-title":"The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction","volume":"12","author":"Moshiri","year":"2022","journal-title":"Sci Rep"},{"key":"2023092216501552100_ref69","article-title":"Docker: lightweight Linux containers for consistent development and deployment","volume":"239","author":"Merkel","year":"2014","journal-title":"Linux J"},{"key":"2023092216501552100_ref70","doi-asserted-by":"crossref","first-page":"1161","DOI":"10.1038\/s41592-021-01254-9","article-title":"Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers","volume":"18","author":"Wratten","year":"2021","journal-title":"Nat Methods"},{"key":"2023092216501552100_ref71","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1186\/s13059-020-02031-1","article-title":"Effects of the COVID-19 pandemic on life scientists","volume":"21","author":"Korbel","year":"2020","journal-title":"Genome Biol"},{"key":"2023092216501552100_ref72","doi-asserted-by":"crossref","first-page":"160018","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR guiding principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci Data"},{"key":"2023092216501552100_ref73","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1038\/nrg.2016.49","article-title":"Coming of age: ten years of next-generation sequencing technologies","volume":"17","author":"Goodwin","year":"2016","journal-title":"Nat Rev Genet"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/24\/5\/bbad280\/51711204\/bbad280.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/24\/5\/bbad280\/51711204\/bbad280.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,22]],"date-time":"2023-09-22T17:07:27Z","timestamp":1695402447000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbad280\/7239892"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,8,9]]},"references-count":73,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2023,9,20]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbad280","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"type":"print","value":"1467-5463"},{"type":"electronic","value":"1477-4054"}],"subject":[],"published-other":{"date-parts":[[2023,9]]},"published":{"date-parts":[[2023,8,9]]},"article-number":"bbad280"}}