StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees
Identifieur interne : 000B81 ( Main/Exploration ); précédent : 000B80; suivant : 000B82StrainSeeker: 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
Affiliations:
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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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Aarestrup</name></author><author><name sortKey="Lund, O" uniqKey="Lund O">O Lund</name></author><author><name sortKey="Sicheritz Ponten, T" uniqKey="Sicheritz Ponten T">T Sicheritz-Pontén</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Steiner, A" uniqKey="Steiner A">A Steiner</name></author><author><name sortKey="Stucki, D" uniqKey="Stucki D">D Stucki</name></author><author><name sortKey="Coscolla, M" uniqKey="Coscolla M">M Coscolla</name></author><author><name sortKey="Borrell, S" uniqKey="Borrell S">S Borrell</name></author><author><name sortKey="Gagneux, S" uniqKey="Gagneux S">S Gagneux</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tamura, K" uniqKey="Tamura K">K Tamura</name></author><author><name sortKey="Stecher, G" uniqKey="Stecher G">G Stecher</name></author><author><name sortKey="Peterson, D" uniqKey="Peterson D">D Peterson</name></author><author><name sortKey="Filipski, A" uniqKey="Filipski A">A Filipski</name></author><author><name sortKey="Kumar, S" uniqKey="Kumar S">S Kumar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tu, Q" uniqKey="Tu Q">Q Tu</name></author><author><name sortKey="He, Z" uniqKey="He Z">Z He</name></author><author><name sortKey="Zhou, J" uniqKey="Zhou J">J Zhou</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wood, De" uniqKey="Wood D">DE Wood</name></author><author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zerbino, Dr" uniqKey="Zerbino D">DR Zerbino</name></author><author><name sortKey="Birney, E" uniqKey="Birney E">E Birney</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Estonie</li></country></list><tree><country name="Estonie"><noRegion><name sortKey="Roosaare, M Rt" sort="Roosaare, M Rt" uniqKey="Roosaare M" first="M Rt" last="Roosaare">M Rt Roosaare</name></noRegion><name sortKey="Andreson, Reidar" sort="Andreson, Reidar" uniqKey="Andreson R" first="Reidar" last="Andreson">Reidar Andreson</name><name sortKey="K Ljalg, Siiri" sort="K Ljalg, Siiri" uniqKey="K Ljalg S" first="Siiri" last="K Ljalg">Siiri K Ljalg</name><name sortKey="K Ljalg, Siiri" sort="K Ljalg, Siiri" uniqKey="K Ljalg S" first="Siiri" last="K Ljalg">Siiri K Ljalg</name><name sortKey="K Ressaar, Triinu" sort="K Ressaar, Triinu" uniqKey="K Ressaar T" first="Triinu" last="K Ressaar">Triinu K Ressaar</name><name sortKey="Kaplinski, Lauris" sort="Kaplinski, Lauris" uniqKey="Kaplinski L" first="Lauris" last="Kaplinski">Lauris Kaplinski</name><name sortKey="Lepamets, Maarja" sort="Lepamets, Maarja" uniqKey="Lepamets M" first="Maarja" last="Lepamets">Maarja Lepamets</name><name sortKey="Mols, M Rt" sort="Mols, M Rt" uniqKey="Mols M" first="M Rt" last="Möls">M Rt Möls</name><name sortKey="Mols, M Rt" sort="Mols, M Rt" uniqKey="Mols M" first="M Rt" last="Möls">M Rt Möls</name><name sortKey="Naaber, Paul" sort="Naaber, Paul" uniqKey="Naaber P" first="Paul" last="Naaber">Paul Naaber</name><name sortKey="Naaber, Paul" sort="Naaber, Paul" uniqKey="Naaber P" first="Paul" last="Naaber">Paul Naaber</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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