RT Journal Article
SR Electronic
T1 StrainSeeker: fast identification of bacterial strains from unassembled sequencing reads using user-provided guide trees
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 040261
DO 10.1101/040261
A1 Roosaare, Märt
A1 Vaher, Mihkel
A1 Kaplinski, Lauris
A1 Möls, Märt
A1 Andreson, Reidar
A1 Lepamets, Maarja
A1 Kõressaar, Triinu
A1 Naaber, Paul
A1 Kõljalg, Siiri
A1 Remm, Maido
YR 2016
UL http://biorxiv.org/content/early/2016/02/19/040261.abstract
AB Background Fast, accurate and high-throughput detection of bacteria is in great demand. The present work was conducted to investigate the possibility of identifying both known and unknown bacterial strains from unassembled next-generation sequencing reads using custom-made guide trees.Results A program named StrainSeeker was developed that constructs a list of specific k-mers for each node of any given Newick-format tree and enables rapid identification of bacterial genomes within minutes. StrainSeeker has been tested and shown to successfully identify Escherichia coli strains from mixed samples in less than 5 minutes. StrainSeeker can also identify bacterial strains from highly diverse metagenomics samples. StrainSeeker is available at http://bioinfo.ut.ee/strainseeker.Conclusions Our novel approach can be useful for both clinical diagnostics and research laboratories because novel bacterial strains are constantly emerging and their fast and accurate detection is very important.bpbase pairNCBINational Center for Biotechnology InformationMLSTmulti-locus sequence typingSRASequence Read ArchiveWGSwhole-genome sequencingUPGMAunweighted pair group method with arithmetic mean