{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T20:14:36Z","timestamp":1787170476591,"version":"build-2736575974"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,8,18]],"date-time":"2021-08-18T00:00:00Z","timestamp":1629244800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"publisher","award":["19-14-00172"],"award-info":[{"award-number":["19-14-00172"]}],"id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Maximizing Investigators\u2019 Research Award","award":["R35 GM138152-01"],"award-info":[{"award-number":["R35 GM138152-01"]}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>The COVID-19 pandemic has ignited a broad scientific interest in viral research in general and coronavirus research in particular. The identification and characterization of viral species in natural reservoirs typically involves de novo assembly. However, existing genome, metagenome and transcriptome assemblers often are not able to assemble many viruses (including coronaviruses) into a single contig. Coverage variation between datasets and within dataset, presence of close strains, splice variants and contamination set a high bar for assemblers to process viral datasets with diverse properties.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We developed coronaSPAdes, a novel assembler for RNA viral species recovery in general and coronaviruses in particular. coronaSPAdes leverages the knowledge about viral genome structures to improve assembly extending ideas initially implemented in biosyntheticSPAdes. We have shown that coronaSPAdes outperforms existing SPAdes modes and other popular short-read metagenome and viral assemblers in the recovery of full-length RNA viral genomes.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>coronaSPAdes version used in this article is a part of SPAdes 3.15 release and is freely available at http:\/\/cab.spbu.ru\/software\/spades.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab597","type":"journal-article","created":{"date-parts":[[2021,8,16]],"date-time":"2021-08-16T07:15:41Z","timestamp":1629098141000},"page":"1-8","source":"Crossref","is-referenced-by-count":71,"title":["coronaSPAdes: from biosynthetic gene clusters to RNA viral assemblies"],"prefix":"10.1093","volume":"38","author":[{"given":"Dmitry","family":"Meleshko","sequence":"first","affiliation":[{"name":"Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medical College , New York, NY 10021, USA"},{"name":"Center for Algorithmic Biotechnology, St. Petersburg State University , St. Peterburg 199004, Russia"},{"name":"Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine of Cornell University , New York, NY 10021, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Iman","family":"Hajirasouliha","sequence":"additional","affiliation":[{"name":"Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine of Cornell University , New York, NY 10021, USA"},{"name":"Englander Institute for Precision Medicine, The Meyer Cancer Center, Weill Cornell Medicine , New York, NY 10021, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2937-9259","authenticated-orcid":false,"given":"Anton","family":"Korobeynikov","sequence":"additional","affiliation":[{"name":"Center for Algorithmic Biotechnology, St. Petersburg State University , St. Peterburg 199004, Russia"},{"name":"Department of Statistical Modelling, St. Petersburg State University , St. Peterburg 198504, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,8,18]]},"reference":[{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"4126","DOI":"10.1093\/bioinformatics\/btaa490","article-title":"MetaviralSPAdes: assembly of viruses from metagenomic data","volume":"36","author":"Antipov","year":"2020","journal-title":"Bioinformatics"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1101\/gr.215038.116","article-title":"De novo assembly of viral quasispecies using overlap graphs","volume":"27","author":"Baaijens","year":"2017","journal-title":"Genome Res"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"530","DOI":"10.12688\/f1000research.18776.1","article-title":"RVDB-prot, a reference viral protein database and its HMM profiles [version 2; peer review: 2 approved]","volume":"8","author":"Bigot","year":"2019","journal-title":"F1000Research"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"D49","DOI":"10.1016\/j.vaccine.2008.07.039","article-title":"The biology of influenza viruses","volume":"26","author":"Bouvier","year":"2008","journal-title":"Vaccine"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"giz100","DOI":"10.1093\/gigascience\/giz100","article-title":"rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data","volume":"8","author":"Bushmanova","year":"2019","journal-title":"GigaScience"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"1781","DOI":"10.1038\/s41564-019-0513-7","article-title":"The structure of the influenza a virus genome","volume":"4","author":"Dadonaite","year":"2019","journal-title":"Nat. Microbiol"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"270","DOI":"10.4161\/rna.8.2.15013","article-title":"Coronaviruses","volume":"8","author":"Denison","year":"2011","journal-title":"RNA Biol"},{"key":"2023033004305352600_","author":"Edgar","year":"2020"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"D427","DOI":"10.1093\/nar\/gky995","article-title":"The Pfam protein families database in 2019","volume":"47","author":"El-Gebali","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1038\/nbt.1883","article-title":"Full-length transcriptome assembly from RNA-seq data without a reference genome","volume":"29","author":"Grabherr","year":"2011","journal-title":"Nat. Biotechnol"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"Quast: quality assessment tool for genome assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"2023033004305352600_","volume-title":"Reference Module in Biomedical Sciences","author":"Harrach","year":"2014"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"2374","DOI":"10.1093\/bioinformatics\/btv120","article-title":"IVA: accurate de novo assembly of RNA virus genomes","volume":"31","author":"Hunt","year":"2015","journal-title":"Bioinformatics"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"3","DOI":"10.24171\/j.phrp.2020.11.1.02","article-title":"Identification of coronavirus isolated from a patient in Korea with COVID-19","volume":"11","author":"Kim","year":"2020","journal-title":"Osong Public Health Res. Perspect"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","article-title":"MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"key":"2023033004305352600_","first-page":"193","author":"Masters","year":"2006"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"1352","DOI":"10.1101\/gr.243477.118","article-title":"Biosyntheticspades: reconstructing biosynthetic gene clusters from assembly graphs","volume":"29","author":"Meleshko","year":"2019","journal-title":"Genome Res"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1038\/s41587-020-00774-7","article-title":"CheckV assesses the quality and completeness of metagenome-assembled viral genomes","volume":"39","author":"Nayfach","year":"2021","journal-title":"Nat. Biotechnol"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"714","DOI":"10.1089\/cmb.2013.0084","article-title":"Assembling single-cell genomes and mini-metagenomes from chimeric MDA products","volume":"20","author":"Nurk","year":"2013","journal-title":"J. Computat. Biol"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"824","DOI":"10.1101\/gr.213959.116","article-title":"metaspades: a new versatile metagenomic assembler","volume":"27","author":"Nurk","year":"2017","journal-title":"Genome Res"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"vey035","DOI":"10.1093\/ve\/vey035","article-title":"Identification and characterization of coronaviridae genomes from vietnamese bats and rats based on conserved protein domains","volume":"4","author":"Phan","year":"2018","journal-title":"Virus Evol"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"e102","DOI":"10.1002\/cpbi.102","article-title":"Using SPAdes de novo assembler","volume":"70","author":"Prjibelski","year":"2020","journal-title":"Curr. Protoc. Bioinf"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"e3817","DOI":"10.7717\/peerj.3817","article-title":"Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity","volume":"5","author":"Roux","year":"2017","journal-title":"PeerJ"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"865","DOI":"10.1534\/g3.113.005967","article-title":"PRICE: software for the targeted assembly of components of (meta) genomic sequence data","volume":"3","author":"Ruby","year":"2013","journal-title":"G3 Genes Genomes Genet"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"e00169-20","DOI":"10.1128\/MRA.00169-20","article-title":"Complete genome sequence of a 2019 novel coronavirus (sars-cov-2) strain isolated in Nepal","volume":"9","author":"Sah","year":"2020","journal-title":"Microbiol. Resource Announc"},{"key":"2023033004305352600_","first-page":"499","volume-title":"Coronaviruses Use Discontinuous Extension for Synthesis of Subgenome-Length Negative Strands","author":"Sawicki","year":"1995"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"2519","DOI":"10.1128\/jvi.64.6.2519-2529.1990","article-title":"Cloning and functional analysis of multiply spliced mRNA species of human immunodeficiency virus type 1","volume":"64","author":"Schwartz","year":"1990","journal-title":"J. Virol"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"e105067","DOI":"10.1371\/journal.pone.0105067","article-title":"Profile hidden Markov models for the detection of viruses within metagenomic sequence data","volume":"9","author":"Skewes-Cox","year":"2014","journal-title":"PLoS One"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/s40168-019-0626-5","article-title":"Choice of assembly software has a critical impact on virome characterisation","volume":"7","author":"Sutton","year":"2019","journal-title":"Microbiome"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"76","DOI":"10.3390\/v10020076","article-title":"RNA dependent RNA polymerases: insights from structure, function and evolution","volume":"10","author":"Venkataraman","year":"2018","journal-title":"Viruses"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"1545","DOI":"10.1101\/gr.247064.118","article-title":"Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis","volume":"29","author":"Viehweger","year":"2019","journal-title":"Genome Res"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1038\/nature08237","article-title":"Architecture and secondary structure of an entire HIV-1 RNA genome","volume":"460","author":"Watts","year":"2009","journal-title":"Nature"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1111\/nyas.12462","article-title":"Continuing challenges in influenza","volume":"1323","author":"Webster","year":"2014","journal-title":"Ann. N. Y. Acad. Sci"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1038\/s41586-020-2008-3","article-title":"A new coronavirus associated with human respiratory disease in china","volume":"579","author":"Wu","year":"2020","journal-title":"Nature"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1186\/1471-2164-13-475","article-title":"De novo assembly of highly diverse viral populations","volume":"13","author":"Yang","year":"2012","journal-title":"BMC Genomics"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"3588","DOI":"10.1016\/j.ygeno.2020.04.016","article-title":"Genotyping coronavirus sars-cov-2: methods and implications","volume":"112","author":"Yin","year":"2020","journal-title":"Genomics"},{"key":"2023033004305352600_","doi-asserted-by":"crossref","first-page":"4380","DOI":"10.1016\/j.cell.2021.06.008","article-title":"Identification of novel bat coronaviruses sheds light on the evolutionary origins of sars-cov-2 and related viruses","volume":"184","author":"Zhou","year":"2021","journal-title":"Cell"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab597\/40301532\/btab597.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/1\/1\/49692584\/btab597.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/1\/1\/49692584\/btab597.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,7]],"date-time":"2023-11-07T07:08:13Z","timestamp":1699340893000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/1\/1\/6354349"}},"subtitle":[],"editor":[{"given":"Peter","family":"Robinson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2021,8,18]]},"references-count":37,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2021,12,22]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab597","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.07.28.224584","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,1,1]]},"published":{"date-parts":[[2021,8,18]]}}}