M&Ms: a versatile software for building microbial mock communities.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
28 03 2022
28 03 2022
Historique:
received:
04
05
2021
revised:
20
12
2021
pubmed:
14
1
2022
medline:
3
2
2023
entrez:
13
1
2022
Statut:
ppublish
Résumé
Advances in sequencing technologies have triggered the development of many bioinformatic tools aimed to analyze 16S rDNA sequencing data. As these tools need to be tested, it is important to simulate datasets that resemble samples from different environments. Here, we introduce M&Ms, a user-friendly open-source bioinformatic tool to produce different 16S rDNA datasets from reference sequences, based on pragmatic ecological parameters. It creates sequence libraries for 'in silico' microbial communities with user-controlled richness, evenness, microdiversity and source environment. M&Ms allows the user to generate simple to complex read datasets based on real parameters that can be used in developing bioinformatic software or in benchmarking current tools. The source code of M&Ms is freely available at https://github.com/ggnatalia/MMs (GPL-3.0 License). Supplementary data are available at Bioinformatics online.
Identifiants
pubmed: 35022654
pii: 6505202
doi: 10.1093/bioinformatics/btab882
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
2057-2059Subventions
Organisme : Spanish Ministerio de Economía, Industria y Competitividad
ID : CTM2016-80095-C2-1-R
Organisme : Spanish Ministerio de Ciencia e Innovación
ID : PID2019-110011RB-C31
Organisme : Severo Ochoa Program at CNB
ID : SEV-2013-0347-17-2
Organisme : European Union's Horizon 2020
Organisme : Marie Skłodowska-Curie
ID : 892961
Informations de copyright
© The Author(s) 2022. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.