VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank.
Identifieur interne : 000663 ( PubMed/Corpus ); précédent : 000662; suivant : 000664VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank.
Auteurs : Ryan C. Shean ; Negar Makhsous ; Graham D. Stoddard ; Michelle J. Lin ; Alexander L. GreningerSource :
- BMC bioinformatics [ 1471-2105 ] ; 2019.
English descriptors
- KwdEn :
- MESH :
- genetics : Genome, Viral.
- methods : Genomics.
- standards : Databases, Nucleic Acid.
- Humans.
Abstract
With sequencing technologies becoming cheaper and easier to use, more groups are able to obtain whole genome sequences of viruses of public health and scientific importance. Submission of genomic data to NCBI GenBank is a requirement prior to publication and plays a critical role in making scientific data publicly available. GenBank currently has automatic prokaryotic and eukaryotic genome annotation pipelines but has no viral annotation pipeline beyond influenza virus. Annotation and submission of viral genome sequence is a non-trivial task, especially for groups that do not routinely interact with GenBank for data submissions.
DOI: 10.1186/s12859-019-2606-y
PubMed: 30674273
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pubmed:30674273Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank.</title><author><name sortKey="Shean, Ryan C" sort="Shean, Ryan C" uniqKey="Shean R" first="Ryan C" last="Shean">Ryan C. Shean</name><affiliation><nlm:affiliation>Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Makhsous, Negar" sort="Makhsous, Negar" uniqKey="Makhsous N" first="Negar" last="Makhsous">Negar Makhsous</name><affiliation><nlm:affiliation>Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Stoddard, Graham D" sort="Stoddard, Graham D" uniqKey="Stoddard G" first="Graham D" last="Stoddard">Graham D. Stoddard</name><affiliation><nlm:affiliation>Department of Neurobiology, University of Washington, Seattle, WA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Lin, Michelle J" sort="Lin, Michelle J" uniqKey="Lin M" first="Michelle J" last="Lin">Michelle J. Lin</name><affiliation><nlm:affiliation>Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Greninger, Alexander L" sort="Greninger, Alexander L" uniqKey="Greninger A" first="Alexander L" last="Greninger">Alexander L. Greninger</name><affiliation><nlm:affiliation>Department of Laboratory Medicine, University of Washington, Seattle, WA, USA. agrening@uw.edu.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2019">2019</date><idno type="RBID">pubmed:30674273</idno><idno type="pmid">30674273</idno><idno type="doi">10.1186/s12859-019-2606-y</idno><idno type="wicri:Area/PubMed/Corpus">000663</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000663</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank.</title><author><name sortKey="Shean, Ryan C" sort="Shean, Ryan C" uniqKey="Shean R" first="Ryan C" last="Shean">Ryan C. Shean</name><affiliation><nlm:affiliation>Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Makhsous, Negar" sort="Makhsous, Negar" uniqKey="Makhsous N" first="Negar" last="Makhsous">Negar Makhsous</name><affiliation><nlm:affiliation>Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Stoddard, Graham D" sort="Stoddard, Graham D" uniqKey="Stoddard G" first="Graham D" last="Stoddard">Graham D. Stoddard</name><affiliation><nlm:affiliation>Department of Neurobiology, University of Washington, Seattle, WA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Lin, Michelle J" sort="Lin, Michelle J" uniqKey="Lin M" first="Michelle J" last="Lin">Michelle J. Lin</name><affiliation><nlm:affiliation>Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Greninger, Alexander L" sort="Greninger, Alexander L" uniqKey="Greninger A" first="Alexander L" last="Greninger">Alexander L. Greninger</name><affiliation><nlm:affiliation>Department of Laboratory Medicine, University of Washington, Seattle, WA, USA. agrening@uw.edu.</nlm:affiliation></affiliation></author></analytic><series><title level="j">BMC bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Databases, Nucleic Acid (standards)</term><term>Genome, Viral (genetics)</term><term>Genomics (methods)</term><term>Humans</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Genome, Viral</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genomics</term></keywords><keywords scheme="MESH" qualifier="standards" xml:lang="en"><term>Databases, Nucleic Acid</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Humans</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">With sequencing technologies becoming cheaper and easier to use, more groups are able to obtain whole genome sequences of viruses of public health and scientific importance. Submission of genomic data to NCBI GenBank is a requirement prior to publication and plays a critical role in making scientific data publicly available. GenBank currently has automatic prokaryotic and eukaryotic genome annotation pipelines but has no viral annotation pipeline beyond influenza virus. Annotation and submission of viral genome sequence is a non-trivial task, especially for groups that do not routinely interact with GenBank for data submissions.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">30674273</PMID><DateCompleted><Year>2019</Year><Month>03</Month><Day>04</Day></DateCompleted><DateRevised><Year>2020</Year><Month>02</Month><Day>25</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2105</ISSN><JournalIssue CitedMedium="Internet"><Volume>20</Volume><Issue>1</Issue><PubDate><Year>2019</Year><Month>Jan</Month><Day>23</Day></PubDate></JournalIssue><Title>BMC bioinformatics</Title><ISOAbbreviation>BMC Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank.</ArticleTitle><Pagination><MedlinePgn>48</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12859-019-2606-y</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">With sequencing technologies becoming cheaper and easier to use, more groups are able to obtain whole genome sequences of viruses of public health and scientific importance. Submission of genomic data to NCBI GenBank is a requirement prior to publication and plays a critical role in making scientific data publicly available. GenBank currently has automatic prokaryotic and eukaryotic genome annotation pipelines but has no viral annotation pipeline beyond influenza virus. Annotation and submission of viral genome sequence is a non-trivial task, especially for groups that do not routinely interact with GenBank for data submissions.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We present Viral Annotation Pipeline and iDentification (VAPiD), a portable and lightweight command-line tool for annotation and GenBank deposition of viral genomes. VAPiD supports annotation of nearly all unsegmented viral genomes. The pipeline has been validated on human immunodeficiency virus, human parainfluenza virus 1-4, human metapneumovirus, human coronaviruses (229E/OC43/NL63/HKU1/SARS/MERS), human enteroviruses/rhinoviruses, measles virus, mumps virus, Hepatitis A-E Virus, Chikungunya virus, dengue virus, and West Nile virus, as well the human polyomaviruses BK/JC/MCV, human adenoviruses, and human papillomaviruses. The program can handle individual or batch submissions of different viruses to GenBank and correctly annotates multiple viruses, including those that contain ribosomal slippage or RNA editing without prior knowledge of the virus to be annotated. VAPiD is programmed in Python and is compatible with Windows, Linux, and Mac OS systems.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">We have created a portable, lightweight, user-friendly, internet-enabled, open-source, command-line genome annotation and submission package to facilitate virus genome submissions to NCBI GenBank. Instructions for downloading and installing VAPiD can be found at https://github.com/rcs333/VAPiD .</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Shean</LastName><ForeName>Ryan C</ForeName><Initials>RC</Initials><AffiliationInfo><Affiliation>Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Makhsous</LastName><ForeName>Negar</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Stoddard</LastName><ForeName>Graham D</ForeName><Initials>GD</Initials><AffiliationInfo><Affiliation>Department of Neurobiology, University of Washington, Seattle, WA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lin</LastName><ForeName>Michelle J</ForeName><Initials>MJ</Initials><AffiliationInfo><Affiliation>Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Greninger</LastName><ForeName>Alexander L</ForeName><Initials>AL</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-7443-0527</Identifier><AffiliationInfo><Affiliation>Department of Laboratory Medicine, University of Washington, Seattle, WA, USA. agrening@uw.edu.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA. agrening@uw.edu.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>01</Month><Day>23</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Bioinformatics</MedlineTA><NlmUniqueID>100965194</NlmUniqueID><ISSNLinking>1471-2105</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D030561" MajorTopicYN="N">Databases, Nucleic Acid</DescriptorName><QualifierName UI="Q000592" MajorTopicYN="Y">standards</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016679" MajorTopicYN="N">Genome, Viral</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="N">Genomics</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Data submission</Keyword><Keyword MajorTopicYN="N">GenBank</Keyword><Keyword MajorTopicYN="N">NCBI</Keyword><Keyword MajorTopicYN="N">VAPiD</Keyword><Keyword MajorTopicYN="N">Viral annotation</Keyword><Keyword MajorTopicYN="N">Viral genomics</Keyword><Keyword MajorTopicYN="N">Virus sequence</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>05</Month><Day>14</Day></PubMedPubDate><PubMedPubDate 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