文献类型： 外文期刊
作者： Hui, Xingqi 1 ; Yang, Jinbao 2 ; Sun, Jinhuan 4 ; Liu, Fang 1 ; Pan, Weihua 2 ;
作者机构： 1.Zhengzhou Univ, Sch Agr Sci, State Key Lab Cotton Biol, Zhengzhou Res Base, Zhengzhou, Peoples R China
2.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Shenzhen Branch, Guangdong Lab Lingnan Modern Agr,Genome Anal Lab M, Shenzhen, Peoples R China
3.Huazhong Agr Univ, Coll Informat, Wuhan, Peoples R China
4.Chinese Acad Sci, Inst Bot, CAS Ctr Excellence Mol Plant Sci, Key Lab Plant Mol Physiol, Beijing, Peoples R China
5.Chinese Acad Agr Sci, Inst Cotton Res, Natl Key Lab Cotton Biobreeding & Integrated Utili, ICR,CAAS, Anyang, Peoples R China
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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