U.S. Department of Energy

Pacific Northwest National Laboratory


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 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.


Produced under funding from the U.S. Department of Energy.


This material was prepared as an account of work sponsored by an agency of the United States Government.  Neither the United States Government nor the United States Department of Energy, nor Battelle, nor any of their employees, nor any jurisdiction or organization that has cooperated in the development of these materials, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness or any information, apparatus, product, software, or process disclosed, or represents that its use would not infringe privately owned rights.

Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or Battelle Memorial Institute. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof.


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under Contract DE-AC05-76RL01830

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