Download
Share
NOT PEER-REVIEWED
"PeerJ Preprints" is a venue for early communication or feedback before peer review. Data may be preliminary.

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

, , , , , , , ,
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.

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Richard Allen White III conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, performed the computation work, reviewed drafts of the paper.

Joseph Brown conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, performed the computation work, reviewed drafts of the paper.

Sean Colby conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, performed the computation work, reviewed drafts of the paper.

Christopher C Overall conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, performed the computation work, reviewed drafts of the paper.

Joon-Yong Lee contributed reagents/materials/analysis tools, performed the computation work, reviewed drafts of the paper.

Jeremy Zucker contributed reagents/materials/analysis tools, performed the computation work, reviewed drafts of the paper.

Kurt R Glaesemann contributed reagents/materials/analysis tools, wrote the paper, performed the computation work, reviewed drafts of the paper.

Christer Jansson wrote the paper, reviewed drafts of the paper.

Janet K Jansson wrote the paper, reviewed drafts of the paper.

Data Deposition

The following information was supplied regarding data availability:

The following information was supplied regarding data availability:

https://github.com/pnnl/atlas

Funding

This research was provided by the PNNL Laboratory-Directed Research and Development (LDRD) Program at PNNL through the Microbiomes in Transition (MinT) Initiative and the Initiative integrated Plant-Atmosphere-Soil System (iPASS) Initiative. PNNL is a national laboratory operated by Battelle for the Department of Energy (DOE) under contract DE-AC06-76RL01830. A portion of the research was conducted using PNNL Institutional Computing (PIC) at PNNL and at EMSL, a national scientific user facility sponsored by the DOE Office of Biological and Environmental Research and located at PNNL. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Add your feedback

Before adding feedback, consider if it can be asked as a question instead, and if so then use the Question tab. Pointing out typos is fine, but authors are encouraged to accept only substantially helpful feedback.

Some Markdown syntax is allowed: _italic_ **bold** ^superscript^ ~subscript~ %%blockquote%% [link text](link URL)
 
By posting this you agree to PeerJ's commenting policies
Download
Content
Alert
Just enter your email

Download article

ATLAS (Automatic Tool for Local Assembly Structures) - a comprehensive infrastructure for assembly, annotation, and genomic binning of metagenomic and metatranscriptomic data
PDF Save to Mendeley RIS XML BibTeX
13 Citations   Views   Downloads