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

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 d...

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Autores principales:	Enzo Guerrero-Araya, Marina Muñoz, César Rodríguez, Daniel Paredes-Sabja
Formato:	article
Lenguaje:	EN
Publicado:	SAGE Publishing 2021
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/44190e03916f474aad18fbbbf3b7c4f8
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id	oai:doaj.org-article:44190e03916f474aad18fbbbf3b7c4f8
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spelling	oai:doaj.org-article:44190e03916f474aad18fbbbf3b7c4f82021-12-01T00:06:08ZFastMLST: A Multi-core Tool for Multilocus Sequence Typing of Draft Genome Assemblies1177-932210.1177/11779322211059238https://doaj.org/article/44190e03916f474aad18fbbbf3b7c4f82021-11-01T00:00:00Zhttps://doi.org/10.1177/11779322211059238https://doaj.org/toc/1177-9322Multilocus 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 varying genome sizes. Compared with other tools such as mlst, CGE/MLST, MLSTar, and PubMLST, FastMLST takes advantage of multiple processors to simultaneously type up to 28 000 genomes in less than 10 minutes, reducing processing times by at least 3-fold with 100% concordance to PubMLST, if contaminated genomes are excluded from the analysis. The source code, installation instructions, and documentation of FastMLST are available at https://github.com/EnzoAndree/FastMLSTEnzo Guerrero-ArayaMarina MuñozCésar RodríguezDaniel Paredes-SabjaSAGE PublishingarticleBiology (General)QH301-705.5ENBioinformatics and Biology Insights, Vol 15 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Enzo Guerrero-Araya Marina Muñoz César Rodríguez Daniel Paredes-Sabja FastMLST: A Multi-core Tool for Multilocus Sequence Typing of Draft Genome Assemblies
description	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 varying genome sizes. Compared with other tools such as mlst, CGE/MLST, MLSTar, and PubMLST, FastMLST takes advantage of multiple processors to simultaneously type up to 28 000 genomes in less than 10 minutes, reducing processing times by at least 3-fold with 100% concordance to PubMLST, if contaminated genomes are excluded from the analysis. The source code, installation instructions, and documentation of FastMLST are available at https://github.com/EnzoAndree/FastMLST
format	article
author	Enzo Guerrero-Araya Marina Muñoz César Rodríguez Daniel Paredes-Sabja
author_facet	Enzo Guerrero-Araya Marina Muñoz César Rodríguez Daniel Paredes-Sabja
author_sort	Enzo Guerrero-Araya
title	FastMLST: A Multi-core Tool for Multilocus Sequence Typing of Draft Genome Assemblies
title_short	FastMLST: A Multi-core Tool for Multilocus Sequence Typing of Draft Genome Assemblies
title_full	FastMLST: A Multi-core Tool for Multilocus Sequence Typing of Draft Genome Assemblies
title_fullStr	FastMLST: A Multi-core Tool for Multilocus Sequence Typing of Draft Genome Assemblies
title_full_unstemmed	FastMLST: A Multi-core Tool for Multilocus Sequence Typing of Draft Genome Assemblies
title_sort	fastmlst: a multi-core tool for multilocus sequence typing of draft genome assemblies
publisher	SAGE Publishing
publishDate	2021
url	https://doaj.org/article/44190e03916f474aad18fbbbf3b7c4f8
work_keys_str_mv	AT enzoguerreroaraya fastmlstamulticoretoolformultilocussequencetypingofdraftgenomeassemblies AT marinamunoz fastmlstamulticoretoolformultilocussequencetypingofdraftgenomeassemblies AT cesarrodriguez fastmlstamulticoretoolformultilocussequencetypingofdraftgenomeassemblies AT danielparedessabja fastmlstamulticoretoolformultilocussequencetypingofdraftgenomeassemblies
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FastMLST: A Multi-core Tool for Multilocus Sequence Typing of Draft Genome Assemblies

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