ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data.
- Kieser S Department of Cell Physiology and Metabolism, Faculty of Medicine, Centre Medical Universitaire, 1206, Geneva, Switzerland.
- Brown J Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
- Zdobnov EM Swiss Institute of Bioinformatics, Geneva, Switzerland.
- Trajkovski M Department of Cell Physiology and Metabolism, Faculty of Medicine, Centre Medical Universitaire, 1206, Geneva, Switzerland.
- McCue LA Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA. leeann.mccue@pnnl.gov.
- 2020-06-24
Published in:
- BMC bioinformatics. - 2020
Analysis workflow
Annotation
Metagenome-assembled genomes
Metagenomics
Metagenome
Metagenomics
Molecular Sequence Annotation
Software
Workflow
English
BACKGROUND
Metagenomics studies provide valuable insight into the composition and function of microbial populations from diverse environments; however, the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for cultured strains yield results that underrepresent the genes and functional potential of uncultured microbes. Recent improvements in sequence assembly methods have eased the reliance on genome databases, thereby allowing the recovery of genomes from uncultured microbes. However, configuring these tools, linking them with advanced binning and annotation tools, and maintaining provenance of the processing continues to be challenging for researchers.
RESULTS
Here we present ATLAS, a software package for customizable data processing from raw sequence reads to functional and taxonomic annotations using state-of-the-art tools to assemble, annotate, quantify, and bin metagenome data. Abundance estimates at genome resolution are provided for each sample in a dataset. ATLAS is written in Python and the workflow implemented in Snakemake; it operates in a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions. The source code for ATLAS is freely available, distributed under a BSD-3 license.
CONCLUSIONS
ATLAS provides a user-friendly, modular and customizable Snakemake workflow for metagenome data processing; it is easily installable with conda and maintained as open-source on GitHub at https://github.com/metagenome-atlas/atlas.
Metagenomics studies provide valuable insight into the composition and function of microbial populations from diverse environments; however, the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for cultured strains yield results that underrepresent the genes and functional potential of uncultured microbes. Recent improvements in sequence assembly methods have eased the reliance on genome databases, thereby allowing the recovery of genomes from uncultured microbes. However, configuring these tools, linking them with advanced binning and annotation tools, and maintaining provenance of the processing continues to be challenging for researchers.
RESULTS
Here we present ATLAS, a software package for customizable data processing from raw sequence reads to functional and taxonomic annotations using state-of-the-art tools to assemble, annotate, quantify, and bin metagenome data. Abundance estimates at genome resolution are provided for each sample in a dataset. ATLAS is written in Python and the workflow implemented in Snakemake; it operates in a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions. The source code for ATLAS is freely available, distributed under a BSD-3 license.
CONCLUSIONS
ATLAS provides a user-friendly, modular and customizable Snakemake workflow for metagenome data processing; it is easily installable with conda and maintained as open-source on GitHub at https://github.com/metagenome-atlas/atlas.
- Language
-
- English
- Open access status
- gold
- Identifiers
-
- DOI 10.1186/s12859-020-03585-4
- PMID 32571209
- Persistent URL
- https://folia.unifr.ch/global/documents/34249
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