Division of Biostatistics, Department of Population Health, New York University School of Medicine, New York, NY 10016, USA.
Bioinformatics. 2023 May 4;39(5). doi: 10.1093/bioinformatics/btad302.
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.
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.
STEMSIM and its tutorial are freely available online at https://github.com/BoyanZhou/STEMSim.
随着宏基因组分析分辨率的提高，纵向宏基因组数据中微生物基因组的进化已成为研究重点。一些软件已经被开发出来，用于在菌株水平上模拟复杂的微生物群落。然而，用于模拟纵向样本中菌株内进化信号的工具仍然缺乏。
在本研究中，我们介绍了 STEMSIM，这是一种用于纵向宏基因组数据的短期进化突变的用户友好型命令行模拟器。输入是微生物群落或单一物种的模拟纵向原始测序读数。输出是带有菌株内进化突变的修改后的读数以及这些突变的相关信息。STEMSIM 将非常有助于评估在宏基因组数据中检测短期进化突变的分析工具。
STEMSIM 及其教程可在 https://github.com/BoyanZhou/STEMSim 上免费获得。
