MAGqual: a stand-alone pipeline to assess the quality of metagenome-assembled genomes.

IF 13.8 1区 生物学 Q1 MICROBIOLOGY Microbiome Pub Date : 2024-11-04 DOI:10.1186/s40168-024-01949-z
Annabel Cansdale, James P J Chong
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Abstract

Background: Metagenomics, the whole genome sequencing of microbial communities, has provided insight into complex ecosystems. It has facilitated the discovery of novel microorganisms, explained community interactions and found applications in various fields. Advances in high-throughput and third-generation sequencing technologies have further fuelled its popularity. Nevertheless, managing the vast data produced and addressing variable dataset quality remain ongoing challenges. Another challenge arises from the number of assembly and binning strategies used across studies. Comparing datasets and analysis tools is complex as it requires the quantitative assessment of metagenome quality. The inherent limitations of metagenomic sequencing, which often involves sequencing complex communities, mean community members are challenging to interrogate with traditional culturing methods leading to many lacking reference sequences. MIMAG standards aim to provide a method to assess metagenome quality for comparison but have not been widely adopted.

Results: To address the need for simple and quick metagenome quality assignation, here we introduce the pipeline MAGqual (Metagenome-Assembled Genome qualifier) and demonstrate its effectiveness at determining metagenomic dataset quality in the context of the MIMAG standards.

Conclusions: The MAGqual pipeline offers an accessible way to evaluate metagenome quality and generate metadata on a large scale. MAGqual is built in Snakemake to ensure readability and scalability, and its open-source nature promotes accessibility, community development, and ease of updates. MAGqual is built in Snakemake, R, and Python and is available under the MIT license on GitHub at https://github.com/ac1513/MAGqual . Video Abstract.

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MAGqual:评估元基因组组装基因组质量的独立管道。
背景:元基因组学是对微生物群落进行全基因组测序的方法,它有助于人们深入了解复杂的生态系统。它促进了新型微生物的发现,解释了群落间的相互作用,并在各个领域得到了应用。高通量和第三代测序技术的进步进一步推动了它的普及。然而,管理所产生的大量数据和解决数据集质量参差不齐的问题仍然是持续存在的挑战。另一个挑战来自于不同研究中使用的组装和分选策略的数量。比较数据集和分析工具非常复杂,因为这需要对元基因组质量进行定量评估。元基因组测序通常涉及复杂群落的测序,其固有的局限性意味着用传统的培养方法询问群落成员具有挑战性,导致许多群落缺乏参考序列。MIMAG 标准旨在提供一种评估元基因组质量的方法,以进行比较,但尚未被广泛采用:为了满足对简单、快速的元基因组质量评估的需求,我们在此介绍了MAGqual(元基因组组装基因组限定器)管道,并展示了它在MIMAG标准背景下确定元基因组数据集质量的有效性:MAGqual 管道为大规模评估元基因组质量和生成元数据提供了一种简便易行的方法。MAGqual 是在 Snakemake 中构建的,以确保可读性和可扩展性,其开源性质促进了可访问性、社区开发和易于更新。MAGqual 使用 Snakemake、R 和 Python 构建,在 MIT 许可下可在 GitHub 上获取:https://github.com/ac1513/MAGqual 。视频摘要。
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来源期刊
Microbiome
Microbiome MICROBIOLOGY-
CiteScore
21.90
自引率
2.60%
发文量
198
审稿时长
4 weeks
期刊介绍: Microbiome is a journal that focuses on studies of microbiomes in humans, animals, plants, and the environment. It covers both natural and manipulated microbiomes, such as those in agriculture. The journal is interested in research that uses meta-omics approaches or novel bioinformatics tools and emphasizes the community/host interaction and structure-function relationship within the microbiome. Studies that go beyond descriptive omics surveys and include experimental or theoretical approaches will be considered for publication. The journal also encourages research that establishes cause and effect relationships and supports proposed microbiome functions. However, studies of individual microbial isolates/species without exploring their impact on the host or the complex microbiome structures and functions will not be considered for publication. Microbiome is indexed in BIOSIS, Current Contents, DOAJ, Embase, MEDLINE, PubMed, PubMed Central, and Science Citations Index Expanded.
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