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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README.md

ATLAS (Automatic Tool for Local Assembly Structures)

DOI

workflow

Documentation

Documentation Status

Install

All dependencies are installed via conda using the bioconda channel. The workflow and some dependencies require Python 3.5.

Using conda

Add the required channels to ensure dependencies can be downloaded:

conda config --add channels conda-forge
conda config --add channels defaults
conda config --add channels r
conda config --add channels bioconda

For more information related to bioconda, see: https://bioconda.github.io/

Installing dependencies:

conda install python=3.5 bbmap click diamond \
    maxbin2 megahit pandas prodigal pyyaml \
    samtools snakemake spades subread

And install ATLAS:

pip install pnnl-atlas

Following install, atlas should be executable:

$ atlas -h
Usage: atlas [OPTIONS] COMMAND [ARGS]...

  ATLAS

Options:
  --version   Show the version and exit.
  -h, --help  Show this message and exit.

Commands:
  assemble      assembly workflow
  download      download reference files
  make-config   prepopulate a configuration file with samples and defaults

Creating an Environment

Not necessary, but this can isolate ATLAS dependencies in a separate work environment. Either clone the repository or download the file, then:

conda env create -f environment.yml

And load and unload that environment using source activate atlas_env and source deactivate atlas_env, respectively.

Getting Started

After installing, one needs to download the required databases and create a sample configuration file.

Databases

To download the databases and their respective metadata databases:

atlas download -o /databases

The downloads use approximately 40 GB of disk space.

Configuration File

To create a simple configuration file (which you can later edit), run:

atlas make-config --database-dir /databases config.yaml /my-data

In this case, 'my-data' is a directory containing .fastq files similar to:

$ tree /my-data
/my-data/
├── Sample-1_R1.fastq.gz
├── Sample-1_R2.fastq.gz
├── Sample-2_R1.fastq.gz
└── Sample-2_R2.fastq.gz

Paired-end, single-end (though some file names still suggest otherwise), and interleaved paired-end FASTQs are supported.

Assembly

After editing your configuration file and adjusting any additional parameters we run assemblies across our samples using:

atlas assemble config.yaml

By default, this will write results into our current working directory across the total number of CPU cores available.

Citing ATLAS

If you are publishing results obtained using ATLAS, please cite:

Richard Allen White III, Joseph Brown, Sean Colby, Christopher C. Overall, Joon-Yong Lee, Jeremy Zucker, Kurt R. Glaesemann, Christer Jansson, Janet K Jansson. 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 https://doi.org/10.7287/peerj.preprints.2843v1.

Richard Allen White III, Joseph Brown, Sean Colby, Christopher C. Overall, Joon-Yong Lee, Jeremy Zucker, Kurt R. Glaesemann, Christer Jansson, Janet K Jansson. ATLAS (Automatic Tool for Local Assembly Structures) - a comprehensive infrastructure for assembly, annotation, and genomic binning of metagenomic and metatranscriptomic data. Bioinformatics. Submitted.

Disclaimer

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.

PACIFIC NORTHWEST NATIONAL LABORATORY operated by BATTELLE for the UNITED STATES DEPARTMENT OF ENERGY under Contract DE-AC05-76RL01830