PT - JOURNAL ARTICLE AU - Märt Roosaare AU - Mihkel Vaher AU - Lauris Kaplinski AU - Märt Möls AU - Reidar Andreson AU - Maarja Lepamets AU - Triinu Kõressaar AU - Paul Naaber AU - Siiri Kõljalg AU - Maido Remm TI - StrainSeeker: fast identification of bacterial strains from unassembled sequencing reads using user-provided guide trees AID - 10.1101/040261 DP - 2016 Jan 01 TA - bioRxiv PG - 040261 4099 - http://biorxiv.org/content/early/2016/02/19/040261.short 4100 - http://biorxiv.org/content/early/2016/02/19/040261.full 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