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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...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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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 |
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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 |