RT Journal Article
SR Electronic
T1 ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 737528
DO 10.1101/737528
A1 Silas Kieser
A1 Joseph Brown
A1 Evgeny M. Zdobnov
A1 Mirko Trajkovski
A1 Lee Ann McCue
YR 2019
UL http://biorxiv.org/content/early/2019/08/20/737528.abstract
AB Background Metagenomics and metatranscriptomics 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 and metatranscriptome data. Genome-centric resolution and abundance estimates 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.Conclusion ATLAS provides a user-friendly, modular and customizable Snakemake workflow for metagenome and metatranscriptome data processing; it is easily installable with conda and maintained as open-source on GitHub at https://github.com/metagenome-atlas/atlas.