# Research Object Crate for Metaenome-Atlas

Original URL: https://workflowhub.eu/workflows/1183/ro_crate?version=1

# 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: ``` 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 https://metagenome-atlas.readthedocs.io/ [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) # Developpment/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.

Author
License
  BSD-3-Clause

## Contents

Main Workflow: Metaenome-Atlas
Size: 1359 bytes
Main Workflow Diagram: resources/images/atlas_image.png
Size: 669191 bytes