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

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1 Biological Sciences Division, Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA
2 Department of Neuroscience, University of Virginia, Charlottesville, Virginia, United States
3 Infomation technology, High Performance Computing (HPC) and Cloud services, Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA
4 Environmental and Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA
DOI
10.7287/peerj.preprints.2843v1
Published
Accepted
Subject Areas
Bioinformatics, Computational Biology, Data Science, Scientific Computing and Simulation, Software Engineering
Keywords
Next-generation sequencing, metagenomics, metatranscriptomics, genome binning, lowest common ancestor (LCA) analysis, Snakemake, Modified Majority Voting-Method (MMVM)
Copyright
© 2017 White III et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
White III RA, Brown J, Colby S, Overall CC, Lee J, Zucker J, Glaesemann KR, Jansson C, Jansson JK. 2017. ATLAS (Automatic Tool for Local Assembly Structures) - a comprehensive infrastructure for assembly, annotation, and genomic binning of metagenomic and metatranscriptomic data. PeerJ Preprints 5:e2843v1

Abstract

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.

Author Comment

Initial version of our manuscript submitted for peer review to Bioinformatics.