StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees

• Published in: PeerJ (San Francisco, CA) Vol. 5; p. e3353
• Main Authors: Roosaare, Märt, Vaher, Mihkel, Kaplinski, Lauris, Möls, Märt, Andreson, Reidar, Lepamets, Maarja, Kõressaar, Triinu, Naaber, Paul, Kõljalg, Siiri, Remm, Maido
• Format: Journal Article
• Language: English
• Published: United States PeerJ. Ltd 18.05.2017; PeerJ, Inc; PeerJ Inc
• Subjects: Algorithms; Bacteria; Bioinformatics; Biology; Blacklisting; Branches; Clade; Classification; Computational Biology; Deoxyribonucleic acid; Diagnostics; DNA; DNA sequencing; E coli; Escherichia coli; Fourier transforms; Genomes; Genomics; Identification; Identification and classification; k-mer; Methods; Microbiology; Shigella; Species identification; Strain identification; Taxonomy; k-mer; Clade; Diagnostics; Species identification; Strain identification
• ISSN: 2167-8359; 2167-8359
• DOI: 10.7717/peerj.3353

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 -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 -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 isolates, we demonstrate that StrainSeeker can predict the clades of with 92% accuracy and correct tree branch assignment with 98% accuracy. Twenty-five thousand Illumina HiSeq reads are sufficient for identification of the strain. 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.