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MCSS：基于结构的微生物群落模拟器

MCSS: microbial community simulator based on structure.

作者信息

Hui Xingqi, Yang Jinbao, Sun Jinhuan, Liu Fang, Pan Weihua

机构信息

Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China.

Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (ICR, CAAS), Shenzhen, China.

出版信息

Front Microbiol. 2024 Mar 7;15:1358257. doi: 10.3389/fmicb.2024.1358257. eCollection 2024.

DOI:10.3389/fmicb.2024.1358257
PMID:38516019
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10956353/
Abstract

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. https://github.com/panlab-bio/mcss.

摘要

组装在宏基因组分析中起着关键作用，而纳入第三代测序技术可显著提高组装结果的完整性和准确性。最近，随着测序技术（Hi-Fi、超长读长）的进步，已经开发了几种基于长读长的生物信息学工具。然而，这些工具的性能和可靠性验证是一个至关重要的问题。为了弥补这一差距，我们提出了MCSS（基于结构的微生物群落模拟器），它能够根据真实微生物群落的结构属性生成模拟微生物群落和测序数据集。评估结果表明，它可以生成与实际群落结构既具有多样性又具有相似性的模拟群落。此外，MCSS为模拟群落中的物种生成合成的PacBio Hi-Fi和牛津纳米孔技术（ONT）长读长。这个创新工具为基准测试和完善宏基因组分析方法提供了宝贵资源。https://github.com/panlab-bio/mcss

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b0d5/10956353/20eb296275eb/fmicb-15-1358257-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b0d5/10956353/c1b5950273a6/fmicb-15-1358257-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b0d5/10956353/aab804cb6d2e/fmicb-15-1358257-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b0d5/10956353/1a494e1c50be/fmicb-15-1358257-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b0d5/10956353/827d107b065d/fmicb-15-1358257-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b0d5/10956353/da17cd68a53b/fmicb-15-1358257-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b0d5/10956353/67480dfbd0a4/fmicb-15-1358257-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b0d5/10956353/49e5077db4fb/fmicb-15-1358257-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b0d5/10956353/20eb296275eb/fmicb-15-1358257-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b0d5/10956353/c1b5950273a6/fmicb-15-1358257-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b0d5/10956353/aab804cb6d2e/fmicb-15-1358257-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b0d5/10956353/1a494e1c50be/fmicb-15-1358257-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b0d5/10956353/827d107b065d/fmicb-15-1358257-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b0d5/10956353/da17cd68a53b/fmicb-15-1358257-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b0d5/10956353/67480dfbd0a4/fmicb-15-1358257-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b0d5/10956353/49e5077db4fb/fmicb-15-1358257-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b0d5/10956353/20eb296275eb/fmicb-15-1358257-g008.jpg

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MCSS: microbial community simulator based on structure.MCSS：基于结构的微生物群落模拟器
Front Microbiol. 2024 Mar 7;15:1358257. doi: 10.3389/fmicb.2024.1358257. eCollection 2024.
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