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FastMLST: A Multi-core Tool for Multilocus Sequence Typing of Draft Genome Assemblies by Enzo Guerrero-Araya; Marina Muñoz; César Rodríguez; Daniel Paredes-Sabja is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

What is FastMLST: A Multi-core Tool for Multilocus Sequence Typing of Draft Genome Assemblies about?

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 profile, and clonal complex or clade (when available), detected for a query, as well as a multi-FASTA file or a series of FASTA files with the concatenated or single allele sequences detected, respectively. FastMLST was validated with 91 different species, with a wide range of guanine-cytosine content (%GC), genome sizes, and fragmentation levels, and a speed test was performed on 3 datasets with var

Who reads FastMLST: A Multi-core Tool for Multilocus Sequence Typing of Draft Genome Assemblies?

Author

Enzo Guerrero-Araya; Marina Muñoz; César Rodríguez; Daniel Paredes-Sabja

Publisher

SAGE Publications

Published

2021

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)