MCSS: microbial community simulator based on structure

文献类型： 外文期刊

第一作者： Hui, Xingqi

作者： Hui, Xingqi;Liu, Fang;Hui, Xingqi;Yang, Jinbao;Pan, Weihua;Yang, Jinbao;Sun, Jinhuan;Liu, Fang

作者机构：

关键词： metagenome; microbiome communities; long reads; simulator; assembly

期刊名称：FRONTIERS IN MICROBIOLOGY （ 影响因子：5.2； 五年影响因子：6.2 ）

ISSN：

年卷期： 2024 年 15 卷

页码：

收录情况： SCI

摘要： De novo assembly plays a pivotal role in metagenomic analysis, and the incorporation of third-generation sequencing technology can significantly improve the integrity and accuracy of assembly results. Recently, with advancements in sequencing technology (Hi-Fi, ultra-long), several long-read-based bioinformatic tools have been developed. However, the validation of the performance and reliability of these tools is a crucial concern. To address this gap, we present MCSS (microbial community simulator based on structure), which has the capability to generate simulated microbial community and sequencing datasets based on the structure attributes of real microbiome communities. The evaluation results indicate that it can generate simulated communities that exhibit both diversity and similarity to actual community structures. Additionally, MCSS generates synthetic PacBio Hi-Fi and Oxford Nanopore Technologies (ONT) long reads for the species within the simulated community. This innovative tool provides a valuable resource for benchmarking and refining metagenomic analysis methods.Code available at: https://github.com/panlab-bio/mcss

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