STRAIN: an R package for multi-locus sequence typing from whole genome sequencing data.

ABSTRACT:

Background

Multi-locus sequence typing (MLST) is a standard typing technique used to associate a sequence type (ST) to a bacterial isolate. When the output of whole genome sequencing (WGS) of a sample is available the ST can be assigned directly processing the read-set. Current approaches employ reads mapping (SRST2) against the MLST loci, k-mer distribution (stringMLST), selective assembly (GRAbB) or whole genome assembly (BIGSdb) followed by BLASTn sequence query. Here we present STRAIN (ST Reduced Assembly IdentificatioN), an R package that implements a hybrid strategy between assembly and mapping of the reads to assign the ST to an isolate starting from its read-sets.

Results

Analysis of 540 publicly accessible Illumina read sets showed STRAIN to be more accurate at corr

SUBMITTER: Dalsass M 

PROVIDER: S-EPMC6873635 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature