https://github.com/metagenome-atlas/atlas

ATLAS - Three commands to start analyzing your metagenome data
https://github.com/metagenome-atlas/atlas

annotation assembly functional-annotation genomic-binning metagenomics snakemake taxonomic-classifications

Last synced: 22 days ago
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ATLAS - Three commands to start analyzing your metagenome data

• Host: GitHub
• URL: https://github.com/metagenome-atlas/atlas
• Owner: metagenome-atlas
• License: bsd-3-clause
• Created: 2016-11-30T15:19:28.000Z (over 8 years ago)
• Default Branch: main
• Last Pushed: 2025-05-08T10:05:23.000Z (29 days ago)
• Last Synced: 2025-05-08T10:46:38.209Z (29 days ago)
• Topics: annotation, assembly, functional-annotation, genomic-binning, metagenomics, snakemake, taxonomic-classifications
• Language: Python
• Homepage: https://metagenome-atlas.github.io/
• Size: 20.3 MB
• Stars: 387
• Watchers: 14
• Forks: 101
• Open Issues: 14
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE.txt

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README

        
# Metagenome-Atlas

[![Anaconda-Server Badge](https://anaconda.org/bioconda/metagenome-atlas/badges/latest_release_relative_date.svg)](https://anaconda.org/bioconda/metagenome-atlas)

[![Bioconda](https://img.shields.io/conda/dn/bioconda/metagenome-atlas.svg?label=Bioconda )](https://anaconda.org/bioconda/metagenome-atlas)

[![Documentation Status](https://readthedocs.org/projects/metagenome-atlas/badge/?version=latest)](https://metagenome-atlas.readthedocs.io/en/latest/?badge=latest)

![Mastodon Follow](https://img.shields.io/mastodon/follow/109273833677404282?domain=https%3A%2F%2Fmstdn.science&style=social)

Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, to Annotation.

![scheme of workflow](resources/images/atlas_list.png?raw=true)

You can start using atlas with three commands:

```sh

    mamba install -y -c bioconda -c conda-forge metagenome-atlas={latest_version}

    atlas init --db-dir databases path/to/fastq/files

    atlas run all

```

where `{latest_version}` should be replaced by [![Version](https://anaconda.org/bioconda/metagenome-atlas/badges/version.svg)](https://anaconda.org/bioconda/metagenome-atlas)

## Webpage

[metagenome-atlas.github.io](https://metagenome-atlas.github.io/)

## Documentation

[Tutorial](https://github.com/metagenome-atlas/Tutorial)

## Citation

> ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data.  

> Kieser, S., Brown, J., Zdobnov, E. M., Trajkovski, M. & McCue, L. A.

> BMC Bioinformatics 21, 257 (2020).  

> doi: [10.1186/s12859-020-03585-4](https://doi.org/10.1186/s12859-020-03585-4)

## Development/Extensions

Here are some ideas I work or want to work on when I have time. If you want to contribute or have some ideas let me know via a feature request issue.

- Optimized MAG recovery (e.g. [Spacegraphcats](https://github.com/spacegraphcats/spacegraphcats))

- Integration of viruses/plasmid that live for now as [extensions](https://github.com/metagenome-atlas/virome_atlas)

- Add statistics and visualisations as in [atlas_analyze](https://github.com/metagenome-atlas/atlas_analyze)

- Implementation of most rules as snakemake wrapper

- Cloud execution

- Update to new Snakemake version and use cool reports.