FastMLST: A Multi-core Tool for Multilocus Sequence Typing of Draft Genome Assemblies.

ABSTRACT: Multilocus Sequence Typing (MLST) is a precise microbial typing approach at the intra-species level for epidemiologic and evolutionary purposes. It operates by assigning a sequence type (ST) identifier to each specimen, based on a combination of alleles of multiple housekeeping genes included in a defined scheme. The use of MLST has multiplied due to the availability of large numbers of genomic sequences and epidemiologic data in public repositories. However, data processing speed has become problematic due to the massive size of modern datasets. Here, we present FastMLST, a tool that is designed to perform PubMLST searches using BLASTn and a divide-and-conquer approach that processes each genome assembly in parallel. The output offered by FastMLST includes a table with the ST, allelic pro

SUBMITTER: Guerrero-Araya E 

PROVIDER: S-EPMC8637782 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature