MentaLiST – A fast MLST caller for large MLST schemes
File(s)mgen000146.pdf (1.15 MB)
Published version
Author(s)
Type
Journal Article
Abstract
MLST (multi-locus sequence typing) is a classic technique for genotyping bacteria, widely applied for pathogen outbreak surveillance. Traditionally, MLST is based on identifying sequence types from a small number of housekeeping genes. With the increasing availability of whole-genome sequencing data, MLST methods have evolved towards larger typing schemes, based on a few hundred genes [core genome MLST (cgMLST)] to a few thousand genes [whole genome MLST (wgMLST)]. Such large-scale MLST schemes have been shown to provide a finer resolution and are increasingly used in various contexts such as hospital outbreaks or foodborne pathogen outbreaks. This methodological shift raises new computational challenges, especially given the large size of the schemes involved. Very few available MLST callers are currently capable of dealing with large MLST schemes. We introduce MentaLiST, a new MLST caller, based on a k-mer voting algorithm and written in the Julia language, specifically designed and implemented to handle large typing schemes. We test it on real and simulated data to show that MentaLiST is faster than any other available MLST caller while providing the same or better accuracy, and is capable of dealing with MLST schemes with up to thousands of genes while requiring limited computational resources. MentaLiST source code and easy installation instructions using a Conda package are available at https://github.com/WGS-TB/MentaLiST.
Date Issued
2018-02-01
Date Acceptance
2017-12-05
Citation
Microbial Genomics, 2018, 4 (2), pp.1-8
ISSN
2057-5858
Publisher
Microbiology Society
Start Page
1
End Page
8
Journal / Book Title
Microbial Genomics
Volume
4
Issue
2
Copyright Statement
© 2020 The Author(s). This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, distribution and reproduction in any medium, provided the original
author and source are credited.
author and source are credited.
License URL
Identifier
https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000146
Subjects
0604 Genetics
0605 Microbiology
Publication Status
Published
Date Publish Online
2018-01-10