Article
STRAIN: an R package for multi-locus sequence typing from whole genome sequencing data.
BMC bioinformatics - 22 Nov 2019
Dalsass Mattia, Bodini Margherita, Lambert Christophe, Mortier Marie-Cécile, Romanelli Marco, Medini Duccio, Muzzi Alessandro, Brozzi Alessandro
Abstract excerpt
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...
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