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

ABSTRACT:

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.

Results

A tool named StrainSeeker was developed that constructs a list of specific k-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 k-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

SUBMITTER: Roosaare M 

PROVIDER: S-EPMC5438578 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature