StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees
Identifieur interne : 001118 ( Pmc/Curation ); précédent : 001117; suivant : 001119StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees
Auteurs : M Rt Roosaare [Estonie] ; Mihkel Vaher [Estonie] ; Lauris Kaplinski [Estonie] ; M Rt Möls [Estonie] ; Reidar Andreson [Estonie] ; Maarja Lepamets [Estonie] ; Triinu K Ressaar [Estonie] ; Paul Naaber [Estonie] ; Siiri K Ljalg [Estonie] ; Maido Remm [Estonie]Source :
- PeerJ [ 2167-8359 ] ; 2017.
Abstract
Fast, accurate and high-throughput identification of bacterial isolates is in great demand. The present work was conducted to investigate the possibility of identifying isolates from unassembled next-generation sequencing reads using custom-made guide trees.
A tool named StrainSeeker was developed that constructs a list of specific
StrainSeeker is a software program that identifies bacterial isolates by assigning them to nodes or leaves of a custom-made guide tree. StrainSeeker’s web interface and pre-computed guide trees are available at
Url:
DOI: 10.7717/peerj.3353
PubMed: 28533988
PubMed Central: 5438578
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strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff-2"><institution>Institute of Mathematical 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="Andreson, Reidar" sort="Andreson, Reidar" uniqKey="Andreson R" first="Reidar" last="Andreson">Reidar Andreson</name><affiliation wicri:level="1"><nlm:aff id="aff-1"><institution>Department of Bioinformatics, 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="Lepamets, Maarja" sort="Lepamets, Maarja" uniqKey="Lepamets M" first="Maarja" last="Lepamets">Maarja Lepamets</name><affiliation wicri:level="1"><nlm:aff 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Eesti</institution>,<addr-line>Tallinn</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-4"><institution>Department of Microbiology, Institute of Biomedicine and Translational Medicine, 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="K Ljalg, Siiri" sort="K Ljalg, Siiri" uniqKey="K Ljalg S" first="Siiri" last="K Ljalg">Siiri K Ljalg</name><affiliation wicri:level="1"><nlm:aff id="aff-4"><institution>Department of Microbiology, Institute of Biomedicine and Translational Medicine, 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-5"><institution>United Laboratories, Tartu University Clinics</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, 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></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">28533988</idno><idno type="pmc">5438578</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5438578</idno><idno type="RBID">PMC:5438578</idno><idno type="doi">10.7717/peerj.3353</idno><date when="2017">2017</date><idno type="wicri:Area/Pmc/Corpus">001118</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001118</idno><idno type="wicri:Area/Pmc/Curation">001118</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">001118</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees</title><author><name sortKey="Roosaare, M Rt" sort="Roosaare, M Rt" uniqKey="Roosaare M" first="M Rt" last="Roosaare">M Rt Roosaare</name><affiliation wicri:level="1"><nlm:aff id="aff-1"><institution>Department of Bioinformatics, 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, 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="Kaplinski, Lauris" sort="Kaplinski, Lauris" uniqKey="Kaplinski L" first="Lauris" last="Kaplinski">Lauris Kaplinski</name><affiliation wicri:level="1"><nlm:aff id="aff-1"><institution>Department of Bioinformatics, 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, 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 Mathematical 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="Andreson, Reidar" sort="Andreson, Reidar" uniqKey="Andreson R" first="Reidar" last="Andreson">Reidar Andreson</name><affiliation wicri:level="1"><nlm:aff id="aff-1"><institution>Department of Bioinformatics, 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="Lepamets, Maarja" sort="Lepamets, Maarja" uniqKey="Lepamets M" first="Maarja" last="Lepamets">Maarja Lepamets</name><affiliation wicri:level="1"><nlm:aff id="aff-1"><institution>Department of Bioinformatics, 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="K Ressaar, Triinu" sort="K Ressaar, Triinu" uniqKey="K Ressaar T" first="Triinu" last="K Ressaar">Triinu K Ressaar</name><affiliation wicri:level="1"><nlm:aff id="aff-1"><institution>Department of Bioinformatics, 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="Naaber, Paul" sort="Naaber, Paul" uniqKey="Naaber P" first="Paul" last="Naaber">Paul Naaber</name><affiliation wicri:level="1"><nlm:aff id="aff-3"><institution>Synlab Eesti</institution>,<addr-line>Tallinn</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-4"><institution>Department of Microbiology, Institute of Biomedicine and Translational Medicine, 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="K Ljalg, Siiri" sort="K Ljalg, Siiri" uniqKey="K Ljalg S" first="Siiri" last="K Ljalg">Siiri K Ljalg</name><affiliation wicri:level="1"><nlm:aff id="aff-4"><institution>Department of Microbiology, Institute of Biomedicine and Translational Medicine, 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-5"><institution>United Laboratories, Tartu University Clinics</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, 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="2017">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Fast, accurate and high-throughput identification of bacterial isolates is in great demand. The present work was conducted to investigate the possibility of identifying isolates from unassembled next-generation sequencing reads using custom-made guide trees.</p></sec><sec><title>Results</title><p>A tool named StrainSeeker was developed that constructs a list of specific <italic>k</italic>-mers for each node of any given Newick-format tree and enables the identification of bacterial isolates in 1–2 min. It uses a novel algorithm, which analyses the observed and expected fractions of node-specific <italic>k</italic>-mers to test the presence of each node in the sample. This allows StrainSeeker to determine where the isolate branches off the guide tree and assign it to a clade whereas other tools assign each read to a reference genome. Using a dataset of 100 <italic>Escherichia coli</italic> isolates, we demonstrate that StrainSeeker can predict the clades of <italic>E. coli</italic> with 92% accuracy and correct tree branch assignment with 98% accuracy. Twenty-five thousand Illumina HiSeq reads are sufficient for identification of the strain.</p></sec><sec><title>Conclusion</title><p>StrainSeeker is a software program that identifies bacterial isolates by assigning them to nodes or leaves of a custom-made guide tree. StrainSeeker’s web interface and pre-computed guide trees are available at <uri xlink:href="http://bioinfo.ut.ee/strainseeker">http://bioinfo.ut.ee/strainseeker</uri>. Source code is stored at GitHub: <uri xlink:href="https://github.com/bioinfo-ut/StrainSeeker">https://github.com/bioinfo-ut/StrainSeeker</uri>.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Ahn, Th" uniqKey="Ahn T">TH Ahn</name></author><author><name sortKey="Chai, J" uniqKey="Chai J">J Chai</name></author><author><name sortKey="Pan, C" uniqKey="Pan C">C Pan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Altschul, Sf" uniqKey="Altschul S">SF Altschul</name></author><author><name sortKey="Madden, Tl" uniqKey="Madden T">TL Madden</name></author><author><name sortKey="Sch Ffer, Aa" uniqKey="Sch Ffer A">AA Schäffer</name></author><author><name sortKey="Zhang, J" uniqKey="Zhang J">J Zhang</name></author><author><name sortKey="Zhang, Z" uniqKey="Zhang Z">Z Zhang</name></author><author><name sortKey="Miller, W" uniqKey="Miller W">W Miller</name></author><author><name sortKey="Lipman, Dj" 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<front><journal-meta><journal-id journal-id-type="nlm-ta">PeerJ</journal-id><journal-id journal-id-type="iso-abbrev">PeerJ</journal-id><journal-id journal-id-type="pmc">PeerJ</journal-id><journal-id journal-id-type="publisher-id">PeerJ</journal-id><journal-title-group><journal-title>PeerJ</journal-title></journal-title-group><issn pub-type="epub">2167-8359</issn><publisher><publisher-name>PeerJ Inc.</publisher-name><publisher-loc>San Francisco, USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">28533988</article-id><article-id pub-id-type="pmc">5438578</article-id><article-id pub-id-type="publisher-id">3353</article-id><article-id pub-id-type="doi">10.7717/peerj.3353</article-id><article-categories><subj-group subj-group-type="heading"><subject>Bioinformatics</subject></subj-group><subj-group subj-group-type="heading"><subject>Computational Biology</subject></subj-group><subj-group subj-group-type="heading"><subject>Microbiology</subject></subj-group></article-categories><title-group><article-title>StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees</article-title></title-group><contrib-group><contrib id="author-1" contrib-type="author" corresp="yes"><name><surname>Roosaare</surname><given-names>Märt</given-names></name><xref ref-type="aff" rid="aff-1">1</xref><email>mrt.roos@gmail.com</email></contrib><contrib id="author-2" contrib-type="author"><name><surname>Vaher</surname><given-names>Mihkel</given-names></name><xref ref-type="aff" rid="aff-1">1</xref></contrib><contrib id="author-3" contrib-type="author"><name><surname>Kaplinski</surname><given-names>Lauris</given-names></name><xref ref-type="aff" rid="aff-1">1</xref></contrib><contrib id="author-4" contrib-type="author"><name><surname>Möls</surname><given-names>Märt</given-names></name><xref ref-type="aff" rid="aff-1">1</xref><xref ref-type="aff" rid="aff-2">2</xref></contrib><contrib id="author-5" contrib-type="author"><name><surname>Andreson</surname><given-names>Reidar</given-names></name><xref ref-type="aff" rid="aff-1">1</xref></contrib><contrib id="author-6" contrib-type="author"><name><surname>Lepamets</surname><given-names>Maarja</given-names></name><xref ref-type="aff" rid="aff-1">1</xref></contrib><contrib id="author-7" contrib-type="author"><name><surname>Kõressaar</surname><given-names>Triinu</given-names></name><xref ref-type="aff" rid="aff-1">1</xref></contrib><contrib id="author-8" contrib-type="author"><name><surname>Naaber</surname><given-names>Paul</given-names></name><xref ref-type="aff" rid="aff-3">3</xref><xref ref-type="aff" rid="aff-4">4</xref></contrib><contrib id="author-9" contrib-type="author"><name><surname>Kõljalg</surname><given-names>Siiri</given-names></name><xref ref-type="aff" rid="aff-4">4</xref><xref ref-type="aff" rid="aff-5">5</xref></contrib><contrib id="author-10" contrib-type="author"><name><surname>Remm</surname><given-names>Maido</given-names></name><xref ref-type="aff" rid="aff-1">1</xref></contrib><aff id="aff-1"><label>1</label><institution>Department of Bioinformatics, University of Tartu</institution>,<addr-line>Tartu</addr-line>,<country>Estonia</country></aff><aff id="aff-2"><label>2</label><institution>Institute of Mathematical Statistics, University of Tartu</institution>,<addr-line>Tartu</addr-line>,<country>Estonia</country></aff><aff id="aff-3"><label>3</label><institution>Synlab Eesti</institution>,<addr-line>Tallinn</addr-line>,<country>Estonia</country></aff><aff id="aff-4"><label>4</label><institution>Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu</institution>,<addr-line>Tartu</addr-line>,<country>Estonia</country></aff><aff id="aff-5"><label>5</label><institution>United Laboratories, Tartu University Clinics</institution>,<addr-line>Tartu</addr-line>,<country>Estonia</country></aff></contrib-group><contrib-group><contrib contrib-type="editor"><name><surname>Lazo</surname><given-names>Gerard</given-names></name></contrib></contrib-group><pub-date pub-type="epub" date-type="pub" iso-8601-date="2017-05-18"><day>18</day><month>5</month><year iso-8601-date="2017">2017</year></pub-date><pub-date pub-type="collection"><year>2017</year></pub-date><volume>5</volume><elocation-id>e3353</elocation-id><history><date date-type="received" iso-8601-date="2017-02-24"><day>24</day><month>2</month><year iso-8601-date="2017">2017</year></date><date date-type="accepted" iso-8601-date="2017-04-26"><day>26</day><month>4</month><year iso-8601-date="2017">2017</year></date></history><permissions><copyright-statement>© 2017 Roosaare et al.</copyright-statement><copyright-year>2017</copyright-year><copyright-holder>Roosaare et al.</copyright-holder><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.</license-p></license></permissions><self-uri xlink:href="https://peerj.com/articles/3353"></self-uri><abstract><sec><title>Background</title><p>Fast, accurate and high-throughput identification of bacterial isolates is in great demand. The present work was conducted to investigate the possibility of identifying isolates from unassembled next-generation sequencing reads using custom-made guide trees.</p></sec><sec><title>Results</title><p>A tool named StrainSeeker was developed that constructs a list of specific <italic>k</italic>-mers for each node of any given Newick-format tree and enables the identification of bacterial isolates in 1–2 min. It uses a novel algorithm, which analyses the observed and expected fractions of node-specific <italic>k</italic>-mers to test the presence of each node in the sample. This allows StrainSeeker to determine where the isolate branches off the guide tree and assign it to a clade whereas other tools assign each read to a reference genome. Using a dataset of 100 <italic>Escherichia coli</italic> isolates, we demonstrate that StrainSeeker can predict the clades of <italic>E. coli</italic> with 92% accuracy and correct tree branch assignment with 98% accuracy. Twenty-five thousand Illumina HiSeq reads are sufficient for identification of the strain.</p></sec><sec><title>Conclusion</title><p>StrainSeeker is a software program that identifies bacterial isolates by assigning them to nodes or leaves of a custom-made guide tree. StrainSeeker’s web interface and pre-computed guide trees are available at <uri xlink:href="http://bioinfo.ut.ee/strainseeker">http://bioinfo.ut.ee/strainseeker</uri>. Source code is stored at GitHub: <uri xlink:href="https://github.com/bioinfo-ut/StrainSeeker">https://github.com/bioinfo-ut/StrainSeeker</uri>.</p></sec></abstract><kwd-group kwd-group-type="author"><kwd><italic>k</italic>-mer</kwd><kwd>Clade</kwd><kwd>Strain identification</kwd><kwd>Species identification</kwd><kwd>Diagnostics</kwd></kwd-group><funding-group><award-group id="fund-1"><funding-source>European Union through the European Regional Development Fund through Estonian Centre of Excellence in Genomics and Translational Medicine</funding-source><award-id>2014-2020.4.01.15-0012, 3.2.0701.11-0013</award-id></award-group><award-group id="fund-2"><funding-source>Estonian Ministry of Education and Research</funding-source><award-id>IUT34-11, SF0180132s08, KOGU-HUMB</award-id></award-group><award-group id="fund-3"><funding-source>Baltic Antibiotic Resistance collaborative Network (BARN)</funding-source></award-group><award-group id="fund-4"><funding-source>Estonian Research Council</funding-source><award-id>IUT34-19</award-id></award-group><award-group id="fund-5"><funding-source>Estonian Science Foundation</funding-source><award-id>9059</award-id></award-group><funding-statement>This work was supported by the European Union through the European Regional Development Fund through Estonian Centre of Excellence in Genomics and Translational Medicine (project No. 2014-2020.4.01.15-0012) and project ARMMD (No. 3.2.0701.11-0013), by the Estonian Ministry of Education and Research (institutional grant IUT34-11, target financing grants SF0180132s08 and KOGU-HUMB), by the Baltic Antibiotic Resistance collaborative Network (BARN), by the Estonian Research Council (grant No. IUT34-19) and by the Estonian Science Foundation (grant No. 9059). There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.</funding-statement></funding-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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