StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees
Identifieur interne : 001A46 ( Ncbi/Checkpoint ); précédent : 001A45; suivant : 001A47StrainSeeker: 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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<author><name sortKey="Remm, Maido" sort="Remm, Maido" uniqKey="Remm M" first="Maido" last="Remm">Maido Remm</name>
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<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>
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</TEI>
<affiliations><list><country><li>Estonie</li>
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</list>
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<name sortKey="K Ljalg, Siiri" sort="K Ljalg, Siiri" uniqKey="K Ljalg S" first="Siiri" last="K Ljalg">Siiri K Ljalg</name>
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<name sortKey="K Ressaar, Triinu" sort="K Ressaar, Triinu" uniqKey="K Ressaar T" first="Triinu" last="K Ressaar">Triinu K Ressaar</name>
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