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      "description": "# Metagenome-Atlas\n\n[![Anaconda-Server Badge](https://anaconda.org/bioconda/metagenome-atlas/badges/latest_release_relative_date.svg)](https://anaconda.org/bioconda/metagenome-atlas)\n[![Bioconda](https://img.shields.io/conda/dn/bioconda/metagenome-atlas.svg?label=Bioconda )](https://anaconda.org/bioconda/metagenome-atlas)\n[![Documentation Status](https://readthedocs.org/projects/metagenome-atlas/badge/?version=latest)](https://metagenome-atlas.readthedocs.io/en/latest/?badge=latest)\n![Mastodon Follow](https://img.shields.io/mastodon/follow/109273833677404282?domain=https%3A%2F%2Fmstdn.science&amp;style=social)\n\n\n\nMetagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, to Annotation.\n\n![scheme of workflow](resources/images/atlas_list.png?raw=true)\n\nYou can start using atlas with three commands:\n```\n    mamba install -y -c bioconda -c conda-forge metagenome-atlas={latest_version}\n    atlas init --db-dir databases path/to/fastq/files\n    atlas run all\n```\nwhere `{latest_version}` should be replaced by [![Version](https://anaconda.org/bioconda/metagenome-atlas/badges/version.svg)](https://anaconda.org/bioconda/metagenome-atlas)\n\n\n# Webpage\n\n[metagenome-atlas.github.io](https://metagenome-atlas.github.io/)\n\n# Documentation\n\nhttps://metagenome-atlas.readthedocs.io/\n\n[Tutorial](https://github.com/metagenome-atlas/Tutorial)\n\n# Citation\n\n&gt; ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data.  \n&gt; Kieser, S., Brown, J., Zdobnov, E. M., Trajkovski, M. &amp; McCue, L. A.   \n&gt; BMC Bioinformatics 21, 257 (2020).  \n&gt; doi: [10.1186/s12859-020-03585-4](https://doi.org/10.1186/s12859-020-03585-4)\n\n\n# Developpment/Extensions\n\nHere 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.\n\n- Optimized MAG recovery (e.g. [Spacegraphcats](https://github.com/spacegraphcats/spacegraphcats))\n- Integration of viruses/plasmid that live for now as [extensions](https://github.com/metagenome-atlas/virome_atlas)\n- Add statistics and visualisations as in [atlas_analyze](https://github.com/metagenome-atlas/atlas_analyze)\n- Implementation of most rules as snakemake wrapper\n- Cloud execution\n- Update to new Snakemake version and use cool reports.\n",
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      "description": "# Metagenome-Atlas\n\n[![Anaconda-Server Badge](https://anaconda.org/bioconda/metagenome-atlas/badges/latest_release_relative_date.svg)](https://anaconda.org/bioconda/metagenome-atlas)\n[![Bioconda](https://img.shields.io/conda/dn/bioconda/metagenome-atlas.svg?label=Bioconda )](https://anaconda.org/bioconda/metagenome-atlas)\n[![Documentation Status](https://readthedocs.org/projects/metagenome-atlas/badge/?version=latest)](https://metagenome-atlas.readthedocs.io/en/latest/?badge=latest)\n![Mastodon Follow](https://img.shields.io/mastodon/follow/109273833677404282?domain=https%3A%2F%2Fmstdn.science&amp;style=social)\n\n\n\nMetagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, to Annotation.\n\n![scheme of workflow](resources/images/atlas_list.png?raw=true)\n\nYou can start using atlas with three commands:\n```\n    mamba install -y -c bioconda -c conda-forge metagenome-atlas={latest_version}\n    atlas init --db-dir databases path/to/fastq/files\n    atlas run all\n```\nwhere `{latest_version}` should be replaced by [![Version](https://anaconda.org/bioconda/metagenome-atlas/badges/version.svg)](https://anaconda.org/bioconda/metagenome-atlas)\n\n\n# Webpage\n\n[metagenome-atlas.github.io](https://metagenome-atlas.github.io/)\n\n# Documentation\n\nhttps://metagenome-atlas.readthedocs.io/\n\n[Tutorial](https://github.com/metagenome-atlas/Tutorial)\n\n# Citation\n\n&gt; ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data.  \n&gt; Kieser, S., Brown, J., Zdobnov, E. M., Trajkovski, M. &amp; McCue, L. A.   \n&gt; BMC Bioinformatics 21, 257 (2020).  \n&gt; doi: [10.1186/s12859-020-03585-4](https://doi.org/10.1186/s12859-020-03585-4)\n\n\n# Developpment/Extensions\n\nHere 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.\n\n- Optimized MAG recovery (e.g. [Spacegraphcats](https://github.com/spacegraphcats/spacegraphcats))\n- Integration of viruses/plasmid that live for now as [extensions](https://github.com/metagenome-atlas/virome_atlas)\n- Add statistics and visualisations as in [atlas_analyze](https://github.com/metagenome-atlas/atlas_analyze)\n- Implementation of most rules as snakemake wrapper\n- Cloud execution\n- Update to new Snakemake version and use cool reports.\n",
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