ATLAS

ATLAS analyzes metagenomic sequence data and integrates genome-wide association studies (GWAS) resources to produce genome-resolved abundance estimates and to characterize genetic architecture across traits.

Key Features:

• Metagenome data processing: Integrated workflow for assembly, annotation, quantification, and binning of metagenomic sequence reads into functional and taxonomic annotations.
• Snakemake workflow: Implemented using Snakemake and runnable on Linux, with support for Python 3.5+ and Anaconda 3+.
• Genome-resolution abundance estimates: Provides abundance estimates at genome resolution for each sample to enable comparative analyses across microbial communities.
• Open-source code: Source code licensed under BSD-3 and available at https://github.com/metagenome-atlas/atlas.
• GWAS querying and visualization: Resource for querying and visualizing hundreds of publicly available GWASs and analyzing genetic architecture features such as pleiotropy, trait-associated loci, and distribution of potential causal variants.

Scientific Applications:

• Metagenomics: Uncover the functional potential and taxonomic composition of microbial populations, including uncultured microbes, from diverse environments.
• Human genetics and GWAS: Characterize genetic architecture of complex traits by surveying pleiotropy, trait-associated loci, and the distribution of potential causal variants across hundreds of GWASs.

Methodology:

Modular Snakemake workflow that integrates assembly, annotation, quantification, and binning tools to produce genome-resolved abundance estimates and records provenance for reproducibility.