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Demo of metagenome Atlas

Metagenome-Atlas is a easy-to-use metagenomic pipeline based on snakemake

It handels all steps from QC, Assembly, Binning, to Annotation.

scheme of workflow

Quick Start Demo

Three commands to start analysing your metagenome data:

    conda install -y -c bioconda -c conda-forge metagenome-atlas
    atlas init --db-dir databases path/to/fastq/files
    atlas run all

All databases and dependencies are installed on the fly. Atlas is based on snakemake which allows to sheddule parts of the workflow to a cluster.

Have a Look asciicast

You want to run these three commands on the example data.

Atlas should be run on a linux sytem, with enough memory (min ~50GB but assembly usually requires 250GB). The only dependency is the conda package manager, which can easy be installed with anaconda.

Get Started

If you have more time, then we recommend you to create a conda environment for atlas to avoid any conflicts of versions.

    conda create -y -n atlasenv
    source activate atlasenv
    conda install -y -c bioconda -c conda-forge metagenome-atlas

And you can run atlas. All other dependencies are installed in specific environments during the run of the pipeline.

We recommend you configure atlas according to your needs.

  • check the samples.tsv
  • edit the config.yaml
  • run atlas on any cluster system

For local execution we have also a docker container

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Cite

We have a BioRxiv preprint please cite:

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data Silas Kieser, Joseph Brown, Evgeny M Zdobnov, Mirko Trajkovski, Lee Ann McCue bioRxiv 737528; doi: https://doi.org/10.1101/737528

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