Cargando…

STEMSIM: a simulator of within-strain short-term evolutionary mutations for longitudinal metagenomic data

MOTIVATION: As the resolution of metagenomic analysis increases, the evolution of microbial genomes in longitudinal metagenomic data has become a research focus. Some software has been developed for the simulation of complex microbial communities at the strain level. However, the tool for simulating...

Descripción completa

Detalles Bibliográficos
Autores principales: Zhou, Boyan, Li, Huilin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10188296/
https://www.ncbi.nlm.nih.gov/pubmed/37154701
http://dx.doi.org/10.1093/bioinformatics/btad302
_version_ 1785042882477948928
author Zhou, Boyan
Li, Huilin
author_facet Zhou, Boyan
Li, Huilin
author_sort Zhou, Boyan
collection PubMed
description MOTIVATION: As the resolution of metagenomic analysis increases, the evolution of microbial genomes in longitudinal metagenomic data has become a research focus. Some software has been developed for the simulation of complex microbial communities at the strain level. However, the tool for simulating within-strain evolutionary signals in longitudinal samples is still lacking. RESULTS: In this study, we introduce STEMSIM, a user-friendly command-line simulator of short-term evolutionary mutations for longitudinal metagenomic data. The input is simulated longitudinal raw sequencing reads of microbial communities or single species. The output is the modified reads with within-strain evolutionary mutations and the relevant information of these mutations. STEMSIM will be of great use for the evaluation of analytic tools that detect short-term evolutionary mutations in metagenomic data. AVAILABILITY AND IMPLEMENTATION: STEMSIM and its tutorial are freely available online at https://github.com/BoyanZhou/STEMSim.
format Online
Article
Text
id pubmed-10188296
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-101882962023-05-18 STEMSIM: a simulator of within-strain short-term evolutionary mutations for longitudinal metagenomic data Zhou, Boyan Li, Huilin Bioinformatics Applications Note MOTIVATION: As the resolution of metagenomic analysis increases, the evolution of microbial genomes in longitudinal metagenomic data has become a research focus. Some software has been developed for the simulation of complex microbial communities at the strain level. However, the tool for simulating within-strain evolutionary signals in longitudinal samples is still lacking. RESULTS: In this study, we introduce STEMSIM, a user-friendly command-line simulator of short-term evolutionary mutations for longitudinal metagenomic data. The input is simulated longitudinal raw sequencing reads of microbial communities or single species. The output is the modified reads with within-strain evolutionary mutations and the relevant information of these mutations. STEMSIM will be of great use for the evaluation of analytic tools that detect short-term evolutionary mutations in metagenomic data. AVAILABILITY AND IMPLEMENTATION: STEMSIM and its tutorial are freely available online at https://github.com/BoyanZhou/STEMSim. Oxford University Press 2023-05-08 /pmc/articles/PMC10188296/ /pubmed/37154701 http://dx.doi.org/10.1093/bioinformatics/btad302 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Zhou, Boyan
Li, Huilin
STEMSIM: a simulator of within-strain short-term evolutionary mutations for longitudinal metagenomic data
title STEMSIM: a simulator of within-strain short-term evolutionary mutations for longitudinal metagenomic data
title_full STEMSIM: a simulator of within-strain short-term evolutionary mutations for longitudinal metagenomic data
title_fullStr STEMSIM: a simulator of within-strain short-term evolutionary mutations for longitudinal metagenomic data
title_full_unstemmed STEMSIM: a simulator of within-strain short-term evolutionary mutations for longitudinal metagenomic data
title_short STEMSIM: a simulator of within-strain short-term evolutionary mutations for longitudinal metagenomic data
title_sort stemsim: a simulator of within-strain short-term evolutionary mutations for longitudinal metagenomic data
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10188296/
https://www.ncbi.nlm.nih.gov/pubmed/37154701
http://dx.doi.org/10.1093/bioinformatics/btad302
work_keys_str_mv AT zhouboyan stemsimasimulatorofwithinstrainshorttermevolutionarymutationsforlongitudinalmetagenomicdata
AT lihuilin stemsimasimulatorofwithinstrainshorttermevolutionarymutationsforlongitudinalmetagenomicdata