MAGqual: A standalone pipeline to assess the quality of metagenome-assembled genomes
MAGqual: A standalone pipeline to assess the quality of metagenome-assembled genomes
复制标题
MAGqual：评估宏基因组组装基因组质量的独立管道
DOI：
10.1101/2023.12.13.571510
复制
发表时间：
2023
期刊：
影响因子：
--
通讯作者：
Cansdale A
中科院分区：
文献类型：
--
作者：
Cansdale A
背景宏基因组学，即微生物群落的全基因组测序，提供了对复杂生态系统的洞察。它促进了新型微生物的发现，解释了群落相互作用并在各个领域找到了应用。高通量和第三代测序技术的进步进一步推动了其普及。然而，管理产生的大量数据和解决可变数据集质量仍然是持续的挑战。另一个挑战来自于研究中使用的组装和装箱策略的数量。比较数据集和分析工具很复杂，因为它需要对宏基因组质量进行定量评估。宏基因组测序通常涉及对复杂的群落进行测序，其固有的局限性意味着群落成员很难用传统的培养方法进行询问，从而导致许多缺乏参考序列。 MIMAG 标准旨在提供一种评估宏基因组质量进行比较的方法，但尚未得到广泛采用。结果为了满足简单快速的宏基因组质量分配的需求，这里我们引入了管道 MAGqual（宏基因组组装基因组限定器），并证明了其在 MIMAG 标准背景下确定宏基因组数据集质量的有效性。结论 MAGqual 管道提供了一种可访问的方法来评估宏基因组质量并大规模生成元数据。 MAGqual 采用 Snakemake 构建，以确保可读性和可扩展性，其开源性质促进了可访问性、社区发展和易于更新。 MAGqual 采用 Snakemake、R 和 Python 构建，可根据 MIT 许可证在 GitHub 上获取：https://github.com/ac1513/MAGqual.Video
BackgroundMetagenomics, 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.ResultsTo 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.ConclusionsThe 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
影响因子：
28.3
作者：
Sieber CMK;Probst AJ;Sharrar A;Thomas BC;Hess M;Tringe SG;Banfield JF
通讯作者：
Banfield JF