ATLAS (Automatic Tool for Local Assembly Structures) - a comprehensive infrastructure for assembly, annotation, and genomic binning of metagenomic and metatranscriptomic data

Summary: ATLAS (Automatic Tool for Local Assembly Structures) is a comprehensive multi-omics data analysis pipeline that is massively parallel and scalable. ATLAS contains a modular analysis pipeline for assembly, annotation, quantification and genome binning of metagenomics and metatranscriptomics data and a framework for reference metaproteomic database construction. ATLAS transforms raw sequence data into functional and taxonomic data at the microbial population level and provides genome-centric resolution through genome binning. ATLAS provides robust taxonomy based on majority voting of protein-coding open reading frames (ORFs) rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS is user-friendly, easy install through bioconda maintained as open-source on GitHub, and is implemented in Snakemake for modular customizable workflows. Availability and implementation: ATLAS is written in python and distributed under a BSD license. ATLAS is compatible with python 3.5+ and anaconda 3+ versions. ATLAS functions on both MacOS and Linux. The source code of ATLAS is freely available at https://github.com/ pnnl /atlas . Contact: Richard Allen White III and Janet Jansson, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA. Email: [email protected] or [email protected], [email protected]