ATLAS (Automatic Tool for Local Assembly Structures)
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/
conda install python=3.5 bbmap click diamond \ maxbin2 megahit pandas prodigal pyyaml \ samtools snakemake spades subread
And install ATLAS:
pip install pnnl-atlas
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
source deactivate atlas_env, respectively.
After installing, one needs to download the required databases and create a sample configuration file.
To download the databases and their respective metadata databases:
atlas download -o /databases
The downloads use approximately 40 GB of disk space.
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.
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.
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.
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