Targeted virus detection in next-generation sequencing data using an automated e-probe based approach.
Identifieur interne : 000359 ( Main/Exploration ); précédent : 000358; suivant : 000360Targeted virus detection in next-generation sequencing data using an automated e-probe based approach.
Auteurs : Marike Visser [Afrique du Sud] ; Johan T. Burger [Afrique du Sud] ; Hans J. Maree [Afrique du Sud]Source :
- Virology [ 1096-0341 ] ; 2016.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Virus, Virus des plantes.
- méthodes : Biologie informatique.
- virologie : Maladies des plantes.
- Génome viral, Jeux de données comme sujet, Logiciel, Sondes d'ADN, Séquençage nucléotidique à haut débit, Variation génétique.
English descriptors
- KwdEn :
- MESH :
- chemical : DNA Probes.
- genetics : Plant Viruses, Viruses.
- methods : Computational Biology.
- virology : Plant Diseases.
- Datasets as Topic, Genetic Variation, Genome, Viral, High-Throughput Nucleotide Sequencing, Software.
Abstract
The use of next-generation sequencing for plant virus detection is rapidly expanding, necessitating the development of bioinformatic pipelines to support analysis of these large datasets. Pipelines need to be easy implementable to mitigate potential insufficient computational infrastructure and/or skills. In this study user-friendly software was developed for the targeted detection of plant viruses based on e-probes. It can be used for both custom e-probe design, as well as screening preloaded probes against raw NGS data for virus detection. The pipeline was compared to de novo assembly-based virus detection in grapevine and produced comparable results, requiring less time and computational resources. The software, named Truffle, is available for the design and screening of e-probes tailored for user-specific virus species and data, along with preloaded probe-sets for grapevine virus detection.
DOI: 10.1016/j.virol.2016.05.008
PubMed: 27209446
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Electronic address: jtb@sun.ac.za.</nlm:affiliation><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>Department of Genetics, Stellenbosch University, Stellenbosch</wicri:regionArea><wicri:noRegion>Stellenbosch</wicri:noRegion></affiliation></author><author><name sortKey="Maree, Hans J" sort="Maree, Hans J" uniqKey="Maree H" first="Hans J" last="Maree">Hans J. Maree</name><affiliation wicri:level="1"><nlm:affiliation>Agricultural Research Council, Infruitec-Nietvoorbij: Institute for Deciduous Fruit, Vines and Wine, Stellenbosch, South Africa; Department of Genetics, Stellenbosch University, Stellenbosch, South Africa. Electronic address: hjmaree@sun.ac.za.</nlm:affiliation><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>Agricultural Research Council, Infruitec-Nietvoorbij: Institute for Deciduous Fruit, Vines and Wine, Stellenbosch, South Africa; Department of Genetics, Stellenbosch University, Stellenbosch</wicri:regionArea><wicri:noRegion>Stellenbosch</wicri:noRegion></affiliation></author></analytic><series><title level="j">Virology</title><idno type="eISSN">1096-0341</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Computational Biology (methods)</term><term>DNA Probes (MeSH)</term><term>Datasets as Topic (MeSH)</term><term>Genetic Variation (MeSH)</term><term>Genome, Viral (MeSH)</term><term>High-Throughput Nucleotide Sequencing (MeSH)</term><term>Plant Diseases (virology)</term><term>Plant Viruses (genetics)</term><term>Software (MeSH)</term><term>Viruses (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Biologie informatique (méthodes)</term><term>Génome viral (MeSH)</term><term>Jeux de données comme sujet (MeSH)</term><term>Logiciel (MeSH)</term><term>Maladies des plantes (virologie)</term><term>Sondes d'ADN (MeSH)</term><term>Séquençage nucléotidique à haut débit (MeSH)</term><term>Variation génétique (MeSH)</term><term>Virus (génétique)</term><term>Virus des plantes (génétique)</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>DNA Probes</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Plant Viruses</term><term>Viruses</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Virus</term><term>Virus des plantes</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Biologie informatique</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Maladies des plantes</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Plant Diseases</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Datasets as Topic</term><term>Genetic Variation</term><term>Genome, Viral</term><term>High-Throughput Nucleotide Sequencing</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Génome viral</term><term>Jeux de données comme sujet</term><term>Logiciel</term><term>Sondes d'ADN</term><term>Séquençage nucléotidique à haut débit</term><term>Variation génétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The use of next-generation sequencing for plant virus detection is rapidly expanding, necessitating the development of bioinformatic pipelines to support analysis of these large datasets. Pipelines need to be easy implementable to mitigate potential insufficient computational infrastructure and/or skills. In this study user-friendly software was developed for the targeted detection of plant viruses based on e-probes. It can be used for both custom e-probe design, as well as screening preloaded probes against raw NGS data for virus detection. The pipeline was compared to de novo assembly-based virus detection in grapevine and produced comparable results, requiring less time and computational resources. The software, named Truffle, is available for the design and screening of e-probes tailored for user-specific virus species and data, along with preloaded probe-sets for grapevine virus detection.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">27209446</PMID><DateCompleted><Year>2017</Year><Month>05</Month><Day>04</Day></DateCompleted><DateRevised><Year>2017</Year><Month>12</Month><Day>19</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1096-0341</ISSN><JournalIssue CitedMedium="Internet"><Volume>495</Volume><PubDate><Year>2016</Year><Month>08</Month></PubDate></JournalIssue><Title>Virology</Title><ISOAbbreviation>Virology</ISOAbbreviation></Journal><ArticleTitle>Targeted virus detection in next-generation sequencing data using an automated e-probe based approach.</ArticleTitle><Pagination><MedlinePgn>122-8</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.virol.2016.05.008</ELocationID><ELocationID EIdType="pii" ValidYN="Y">S0042-6822(16)30117-9</ELocationID><Abstract><AbstractText>The use of next-generation sequencing for plant virus detection is rapidly expanding, necessitating the development of bioinformatic pipelines to support analysis of these large datasets. Pipelines need to be easy implementable to mitigate potential insufficient computational infrastructure and/or skills. In this study user-friendly software was developed for the targeted detection of plant viruses based on e-probes. It can be used for both custom e-probe design, as well as screening preloaded probes against raw NGS data for virus detection. The pipeline was compared to de novo assembly-based virus detection in grapevine and produced comparable results, requiring less time and computational resources. The software, named Truffle, is available for the design and screening of e-probes tailored for user-specific virus species and data, along with preloaded probe-sets for grapevine virus detection.</AbstractText><CopyrightInformation>Copyright © 2016 Elsevier Inc. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Visser</LastName><ForeName>Marike</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Agricultural Research Council, Infruitec-Nietvoorbij: Institute for Deciduous Fruit, Vines and Wine, Stellenbosch, South Africa; Department of Genetics, Stellenbosch University, Stellenbosch, South Africa. Electronic address: visserm@arc.agric.za.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Burger</LastName><ForeName>Johan T</ForeName><Initials>JT</Initials><AffiliationInfo><Affiliation>Department of Genetics, Stellenbosch University, Stellenbosch, South Africa. Electronic address: jtb@sun.ac.za.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Maree</LastName><ForeName>Hans J</ForeName><Initials>HJ</Initials><AffiliationInfo><Affiliation>Agricultural Research Council, Infruitec-Nietvoorbij: Institute for Deciduous Fruit, Vines and Wine, Stellenbosch, South Africa; Department of Genetics, Stellenbosch University, Stellenbosch, South Africa. Electronic address: hjmaree@sun.ac.za.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>05</Month><Day>20</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Virology</MedlineTA><NlmUniqueID>0110674</NlmUniqueID><ISSNLinking>0042-6822</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D015342">DNA Probes</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015342" MajorTopicYN="Y">DNA Probes</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D066264" MajorTopicYN="N">Datasets as Topic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="N">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016679" MajorTopicYN="N">Genome, Viral</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="Y">High-Throughput Nucleotide Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="N">Plant Diseases</DescriptorName><QualifierName UI="Q000821" MajorTopicYN="N">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010942" MajorTopicYN="N">Plant Viruses</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012984" MajorTopicYN="Y">Software</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014780" MajorTopicYN="N">Viruses</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Bioinformatics</Keyword><Keyword MajorTopicYN="Y">Grapevine</Keyword><Keyword MajorTopicYN="Y">Grapevine leafroll disease</Keyword><Keyword MajorTopicYN="Y">High-throughput sequencing</Keyword><Keyword MajorTopicYN="Y">Virus diagnostics</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year><Month>02</Month><Day>19</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2016</Year><Month>05</Month><Day>05</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2016</Year><Month>05</Month><Day>12</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>5</Month><Day>23</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>5</Month><Day>23</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2017</Year><Month>5</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">27209446</ArticleId><ArticleId IdType="pii">S0042-6822(16)30117-9</ArticleId><ArticleId IdType="doi">10.1016/j.virol.2016.05.008</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Afrique du Sud</li></country></list><tree><country name="Afrique du Sud"><noRegion><name sortKey="Visser, Marike" sort="Visser, Marike" uniqKey="Visser M" first="Marike" last="Visser">Marike Visser</name></noRegion><name sortKey="Burger, Johan T" sort="Burger, Johan T" uniqKey="Burger J" first="Johan T" last="Burger">Johan T. Burger</name><name sortKey="Maree, Hans J" sort="Maree, Hans J" uniqKey="Maree H" first="Hans J" last="Maree">Hans J. Maree</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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