ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data
ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data
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DOI：
10.1186/s12859-020-03585-4
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发表时间：
2020-06-22
影响因子：
3
通讯作者：
McCue, Lee Ann
中科院分区：
文献类型：
--
作者：
Kieser, Silas;Brown, Joseph;McCue, Lee Ann
背景
宏基因组学研究为了解不同环境中微生物种群的组成和功能提供了有价值的见解；然而，那些依赖于将读段映射到基因目录或培养菌株的基因组数据库的数据处理流程所产生的结果，低估了未培养微生物的基因和功能潜力。序列组装方法的近期改进缓解了对基因组数据库的依赖，从而能够从未培养微生物中恢复基因组。然而，配置这些工具，将它们与先进的分箱和注释工具相连接，并维护处理过程的溯源信息，对研究人员来说仍然具有挑战性。
结果
在此我们介绍ATLAS，这是一个软件包，它使用最先进的工具对原始序列读段进行可定制的数据处理，直至获得功能和分类学注释，包括组装、注释、定量和对宏基因组数据进行分箱。为数据集中的每个样本提供了基因组分辨率下的丰度估计。ATLAS是用Python编写的，工作流程在Snakemake中实现；它在Linux环境中运行，并且与Python 3.5及以上版本和Anaconda 3及以上版本兼容。ATLAS的源代码可免费获取，依据BSD - 3许可证分发。
结论
ATLAS为宏基因组数据处理提供了一个用户友好、模块化且可定制的Snakemake工作流程；它可以通过conda轻松安装，并作为开源项目在GitHub（https://github.com/metagenome-atlas/atlas）上维护。
Background Metagenomics studies provide valuable insight into the composition and function of microbial populations from diverse environments; however, the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for cultured strains yield results that underrepresent the genes and functional potential of uncultured microbes. Recent improvements in sequence assembly methods have eased the reliance on genome databases, thereby allowing the recovery of genomes from uncultured microbes. However, configuring these tools, linking them with advanced binning and annotation tools, and maintaining provenance of the processing continues to be challenging for researchers. Results Here we present ATLAS, a software package for customizable data processing from raw sequence reads to functional and taxonomic annotations using state-of-the-art tools to assemble, annotate, quantify, and bin metagenome data. Abundance estimates at genome resolution are provided for each sample in a dataset. ATLAS is written in Python and the workflow implemented in Snakemake; it operates in a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions. The source code for ATLAS is freely available, distributed under a BSD-3 license. Conclusions ATLAS provides a user-friendly, modular and customizable Snakemake workflow for metagenome data processing; it is easily installable with conda and maintained as open-source on GitHub at https://github.com/metagenome-atlas/atlas.