StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees.
Identifieur interne : 000C86 ( PubMed/Curation ); précédent : 000C85; suivant : 000C87StrainSeeker: 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.
DOI: 10.7717/peerj.3353
PubMed: 28533988
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<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>
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<ArticleTitle>StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees.</ArticleTitle>
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<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>
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<Author ValidYN="Y"><LastName>Vaher</LastName>
<ForeName>Mihkel</ForeName>
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<AffiliationInfo><Affiliation>Department of Bioinformatics, University of Tartu, Tartu, Estonia.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Kaplinski</LastName>
<ForeName>Lauris</ForeName>
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<AffiliationInfo><Affiliation>Department of Bioinformatics, University of Tartu, Tartu, Estonia.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Möls</LastName>
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<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>
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<AffiliationInfo><Affiliation>Department of Bioinformatics, University of Tartu, Tartu, Estonia.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Lepamets</LastName>
<ForeName>Maarja</ForeName>
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<AffiliationInfo><Affiliation>Department of Bioinformatics, University of Tartu, Tartu, Estonia.</Affiliation>
</AffiliationInfo>
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</AffiliationInfo>
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<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>
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<Language>eng</Language>
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<KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Clade</Keyword>
<Keyword MajorTopicYN="N">Diagnostics</Keyword>
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<ReferenceList><Reference><Citation>Nucleic Acids Res. 2014 Apr;42(8):e67</Citation>
<ArticleIdList><ArticleId IdType="pubmed">24523352</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Proc Natl Acad Sci U S A. 2014 Apr 15;111(15):5694-9</Citation>
<ArticleIdList><ArticleId IdType="pubmed">24706808</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>BMC Bioinformatics. 2015 Nov 04;16:363</Citation>
<ArticleIdList><ArticleId IdType="pubmed">26537885</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Genome Res. 2008 May;18(5):821-9</Citation>
<ArticleIdList><ArticleId IdType="pubmed">18349386</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Rapid Commun Mass Spectrom. 2013 Feb 15;27(3):409-18</Citation>
<ArticleIdList><ArticleId IdType="pubmed">23280972</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Proc Natl Acad Sci U S A. 2009 Oct 20;106(42):17939-44</Citation>
<ArticleIdList><ArticleId IdType="pubmed">19815525</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Mol Biol Evol. 2013 Dec;30(12):2725-9</Citation>
<ArticleIdList><ArticleId IdType="pubmed">24132122</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Clin Microbiol. 2014 Jan;52(1):139-46</Citation>
<ArticleIdList><ArticleId IdType="pubmed">24172157</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Microbes Infect. 2002 Sep;4(11):1125-32</Citation>
<ArticleIdList><ArticleId IdType="pubmed">12361912</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Clin Microbiol. 2012 Apr;50(4):1355-61</Citation>
<ArticleIdList><ArticleId IdType="pubmed">22238442</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nucleic Acids Res. 2002 Jul 15;30(14):3059-66</Citation>
<ArticleIdList><ArticleId IdType="pubmed">12136088</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>BMC Genomics. 2015 Mar 25;16:236</Citation>
<ArticleIdList><ArticleId IdType="pubmed">25879410</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Sci Rep. 2016 Jan 18;6:19233</Citation>
<ArticleIdList><ArticleId IdType="pubmed">26778510</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Gigascience. 2015 Dec 03;4:58</Citation>
<ArticleIdList><ArticleId IdType="pubmed">26640690</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>BMC Genomics. 2014 Oct 09;15:881</Citation>
<ArticleIdList><ArticleId IdType="pubmed">25297886</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Bioinformatics. 2015 Jan 15;31(2):170-7</Citation>
<ArticleIdList><ArticleId IdType="pubmed">25266224</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Genome Biol. 2016 Jun 20;17(1):132</Citation>
<ArticleIdList><ArticleId IdType="pubmed">27323842</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nat Commun. 2015 Dec 21;6:10063</Citation>
<ArticleIdList><ArticleId IdType="pubmed">26686880</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Genome Med. 2014 Nov 20;6(11):90</Citation>
<ArticleIdList><ArticleId IdType="pubmed">25422674</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Genome Biol. 2014 Mar 03;15(3):R46</Citation>
<ArticleIdList><ArticleId IdType="pubmed">24580807</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nucleic Acids Res. 1997 Sep 1;25(17):3389-402</Citation>
<ArticleIdList><ArticleId IdType="pubmed">9254694</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>BMC Bioinformatics. 2015 Nov 25;16:398</Citation>
<ArticleIdList><ArticleId IdType="pubmed">26608174</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Annu Rev Microbiol. 2006;60:561-88</Citation>
<ArticleIdList><ArticleId IdType="pubmed">16774461</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
</PubmedData>
</pubmed>
</record>
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