PlasmidSeeker: identification of known plasmids from bacterial whole genome sequencing reads
Identifieur interne : 000858 ( Main/Exploration ); précédent : 000857; suivant : 000859PlasmidSeeker: identification of known plasmids from bacterial whole genome sequencing reads
Auteurs : M Rt Roosaare [Estonie] ; Mikk Puustusmaa [Estonie] ; M Rt Möls [Estonie] ; Mihkel Vaher [Estonie] ; Maido Remm [Estonie]Source :
- PeerJ [ 2167-8359 ] ; 2018.
Abstract
Plasmids play an important role in the dissemination of antibiotic resistance, making their detection an important task. Using whole genome sequencing (WGS), it is possible to capture both bacterial and plasmid sequence data, but short read lengths make plasmid detection a complex problem.
We developed a tool named PlasmidSeeker that enables the detection of plasmids from bacterial WGS data without read assembly. The PlasmidSeeker algorithm is based on
PlasmidSeeker enables quick detection of known plasmids and complements existing tools that assemble plasmids de novo. The PlasmidSeeker source code is stored on GitHub:
Url:
DOI: 10.7717/peerj.4588
PubMed: 29629246
PubMed Central: 5885972
Affiliations:
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strict</wicri:regionArea></affiliation></author><author><name sortKey="Puustusmaa, Mikk" sort="Puustusmaa, Mikk" uniqKey="Puustusmaa M" first="Mikk" last="Puustusmaa">Mikk Puustusmaa</name><affiliation wicri:level="1"><nlm:aff id="aff-1"><institution>Department of Bioinformatics, IMCB, University of Tartu</institution>,<addr-line>Tartu</addr-line>,<country>Estonia</country></nlm:aff><country xml:lang="fr">Estonie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Mols, M Rt" sort="Mols, M Rt" uniqKey="Mols M" first="M Rt" last="Möls">M Rt Möls</name><affiliation wicri:level="1"><nlm:aff id="aff-1"><institution>Department of Bioinformatics, IMCB, University of Tartu</institution>,<addr-line>Tartu</addr-line>,<country>Estonia</country></nlm:aff><country xml:lang="fr">Estonie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff-2"><institution>Institute of Mathematics and Statistics, University of Tartu</institution>,<addr-line>Tartu</addr-line>,<country>Estonia</country></nlm:aff><country xml:lang="fr">Estonie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Vaher, Mihkel" sort="Vaher, Mihkel" uniqKey="Vaher M" first="Mihkel" last="Vaher">Mihkel Vaher</name><affiliation wicri:level="1"><nlm:aff id="aff-1"><institution>Department of Bioinformatics, IMCB, University of Tartu</institution>,<addr-line>Tartu</addr-line>,<country>Estonia</country></nlm:aff><country xml:lang="fr">Estonie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Remm, Maido" sort="Remm, Maido" uniqKey="Remm M" first="Maido" last="Remm">Maido Remm</name><affiliation wicri:level="1"><nlm:aff id="aff-1"><institution>Department of Bioinformatics, IMCB, University of Tartu</institution>,<addr-line>Tartu</addr-line>,<country>Estonia</country></nlm:aff><country xml:lang="fr">Estonie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">PeerJ</title><idno type="eISSN">2167-8359</idno><imprint><date when="2018">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Plasmids play an important role in the dissemination of antibiotic resistance, making their detection an important task. Using whole genome sequencing (WGS), it is possible to capture both bacterial and plasmid sequence data, but short read lengths make plasmid detection a complex problem.</p></sec><sec><title>Results</title><p>We developed a tool named PlasmidSeeker that enables the detection of plasmids from bacterial WGS data without read assembly. The PlasmidSeeker algorithm is based on <italic>k</italic>-mers and uses <italic>k</italic>-mer abundance to distinguish between plasmid and bacterial sequences. We tested the performance of PlasmidSeeker on a set of simulated and real bacterial WGS samples, resulting in 100% sensitivity and 99.98% specificity.</p></sec><sec><title>Conclusion</title><p>PlasmidSeeker enables quick detection of known plasmids and complements existing tools that assemble plasmids de novo. The PlasmidSeeker source code is stored on GitHub: <uri xlink:href="https://github.com/bioinfo-ut/PlasmidSeeker">https://github.com/bioinfo-ut/PlasmidSeeker</uri>.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Antipov, D" uniqKey="Antipov D">D Antipov</name></author><author><name sortKey="Hartwick, N" uniqKey="Hartwick N">N Hartwick</name></author><author><name sortKey="Shen, M" uniqKey="Shen M">M Shen</name></author><author><name sortKey="Raiko, M" uniqKey="Raiko M">M Raiko</name></author><author><name sortKey="Lapidus, A" uniqKey="Lapidus A">A Lapidus</name></author><author><name sortKey="Pevzner, P" uniqKey="Pevzner P">P Pevzner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Carattoli, A" uniqKey="Carattoli A">A Carattoli</name></author><author><name sortKey="Zankari, E" uniqKey="Zankari E">E Zankari</name></author><author><name sortKey="Garcia Fernandez, A" uniqKey="Garcia Fernandez 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last="Puustusmaa">Mikk Puustusmaa</name><name sortKey="Remm, Maido" sort="Remm, Maido" uniqKey="Remm M" first="Maido" last="Remm">Maido Remm</name><name sortKey="Vaher, Mihkel" sort="Vaher, Mihkel" uniqKey="Vaher M" first="Mihkel" last="Vaher">Mihkel Vaher</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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