ATLAS
Description:
ATLAS (Automatic Tool for Local Assembly Structures) is a comprehensive pipeline that is massively parallel, scalable, and modular analysis pipeline for assembly, annotation, quantification and genome binning of Next-Generation Sequencing (NGS) metagenomics, metatranscriptomics, and a framework for reference metaproteomic database construction. ATLAS transforms raw NGS data into functional, taxonomic, taxonomy by function abundances at the microbial population level and provides genome-centric resolution using binning. ATLAS provides robust taxonomy of based on majority voting of protein-coding open reading frames 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 work-flows.
Acknowledgement:
Produced under funding from the U.S. Department of Energy.
Disclaimer:
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