StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees.
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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.
DOI: 10.7717/peerj.3353
PubMed: 28533988
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Andreson</name><affiliation wicri:level="1"><nlm:affiliation>Department of Bioinformatics, University of Tartu, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Department of Bioinformatics, University of Tartu, Tartu</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:affiliation>Department of Bioinformatics, University of Tartu, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Department of Bioinformatics, University of Tartu, Tartu</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:affiliation>Department of Bioinformatics, University of Tartu, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Department of Bioinformatics, University of Tartu, Tartu</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:affiliation>Synlab Eesti, Tallinn, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Synlab Eesti, Tallinn</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:affiliation>Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu</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:affiliation>Department of Bioinformatics, University of Tartu, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Department of Bioinformatics, University of Tartu, Tartu</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2017">2017</date><idno type="RBID">pubmed:28533988</idno><idno type="pmid">28533988</idno><idno type="doi">10.7717/peerj.3353</idno><idno type="wicri:Area/PubMed/Corpus">000C86</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000C86</idno><idno type="wicri:Area/PubMed/Curation">000C86</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000C86</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">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:affiliation>Department of Bioinformatics, University of Tartu, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Department of Bioinformatics, University of Tartu, Tartu</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:affiliation>Department of Bioinformatics, University of Tartu, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Department of Bioinformatics, University of Tartu, Tartu</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:affiliation>Department of Bioinformatics, University of Tartu, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Department of Bioinformatics, University of Tartu, Tartu</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:affiliation>Department of Bioinformatics, University of Tartu, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Department of Bioinformatics, University of Tartu, Tartu</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:affiliation>Department of Bioinformatics, University of Tartu, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Department of Bioinformatics, University of Tartu, Tartu</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:affiliation>Department of Bioinformatics, University of Tartu, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Department of Bioinformatics, University of Tartu, Tartu</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:affiliation>Department of Bioinformatics, University of Tartu, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Department of Bioinformatics, University of Tartu, Tartu</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:affiliation>Synlab Eesti, Tallinn, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Synlab Eesti, Tallinn</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:affiliation>Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu</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:affiliation>Department of Bioinformatics, University of Tartu, Tartu, Estonia.</nlm:affiliation><country xml:lang="fr">Estonie</country><wicri:regionArea>Department of Bioinformatics, University of Tartu, Tartu</wicri:regionArea></affiliation></author></analytic><series><title level="j">PeerJ</title><idno type="ISSN">2167-8359</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">28533988</PMID><DateRevised><Year>2019</Year><Month>11</Month><Day>20</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">2167-8359</ISSN><JournalIssue CitedMedium="Print"><Volume>5</Volume><PubDate><Year>2017</Year></PubDate></JournalIssue><Title>PeerJ</Title><ISOAbbreviation>PeerJ</ISOAbbreviation></Journal><ArticleTitle>StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees.</ArticleTitle><Pagination><MedlinePgn>e3353</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.7717/peerj.3353</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">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.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">A tool named StrainSeeker was developed that constructs a list of specific <i>k</i>-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 <i>k</i>-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 <i>Escherichia coli</i> isolates, we demonstrate that StrainSeeker can predict the clades of <i>E. coli</i> with 92% accuracy and correct tree branch assignment with 98% accuracy. Twenty-five thousand Illumina HiSeq reads are sufficient for identification of the strain.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">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 http://bioinfo.ut.ee/strainseeker. Source code is stored at GitHub: https://github.com/bioinfo-ut/StrainSeeker.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Roosaare</LastName><ForeName>Märt</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Bioinformatics, University of Tartu, Tartu, Estonia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vaher</LastName><ForeName>Mihkel</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Bioinformatics, University of Tartu, Tartu, Estonia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kaplinski</LastName><ForeName>Lauris</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Department of Bioinformatics, University of Tartu, Tartu, Estonia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Möls</LastName><ForeName>Märt</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Bioinformatics, University of Tartu, Tartu, Estonia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institute of Mathematical Statistics, University of Tartu, Tartu, Estonia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Andreson</LastName><ForeName>Reidar</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Department of Bioinformatics, University of Tartu, Tartu, Estonia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lepamets</LastName><ForeName>Maarja</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Bioinformatics, University of Tartu, Tartu, Estonia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kõressaar</LastName><ForeName>Triinu</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Department of Bioinformatics, University of Tartu, Tartu, Estonia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Naaber</LastName><ForeName>Paul</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Synlab Eesti, Tallinn, Estonia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kõljalg</LastName><ForeName>Siiri</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>United Laboratories, Tartu University Clinics, Tartu, Estonia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Remm</LastName><ForeName>Maido</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Bioinformatics, University of Tartu, Tartu, Estonia.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>figshare</DataBankName><AccessionNumberList><AccessionNumber>10.6084/m9.figshare.c.3750794.v1</AccessionNumber></AccessionNumberList></DataBank></DataBankList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>05</Month><Day>18</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PeerJ</MedlineTA><NlmUniqueID>101603425</NlmUniqueID><ISSNLinking>2167-8359</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Clade</Keyword><Keyword MajorTopicYN="N">Diagnostics</Keyword><Keyword MajorTopicYN="N">Species identification</Keyword><Keyword MajorTopicYN="N">Strain identification</Keyword><Keyword MajorTopicYN="N">k-mer</Keyword></KeywordList><CoiStatement>Paul Naaber is an employee of Synlab Eesti, Tallinn, Estonia.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>02</Month><Day>24</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>04</Month><Day>26</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>5</Month><Day>24</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>5</Month><Day>24</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2017</Year><Month>5</Month><Day>24</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">28533988</ArticleId><ArticleId IdType="doi">10.7717/peerj.3353</ArticleId><ArticleId IdType="pii">3353</ArticleId><ArticleId IdType="pmc">PMC5438578</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Nucleic 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