数字农科院2.0

MCSS: microbial community simulator based on structure

文献类型： 外文期刊

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

作者机构：

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

期刊名称： Frontiers in Microbiology

ISSN： 1664-302X

年卷期： 2024 年 15 卷

页码：

收录情况： SCIE（2024版）

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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