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ATLAS

Quick Start

Three commands to start analysing your metagenome data:

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

All databases and dependencies are installed on the fly in the directory --db-dir. You want to run this three commands on the example_data on the GitHub repo. If you have more time, then we recommend you to configure atlas according to your needs:

Atlas is a workflow for assembly and binning of metagenomic reads

Documentation

.. toctree::
    :maxdepth: 1
    :caption: Setup

    usage/getting_started
    usage/cluster
    usage/test

.. toctree::
    :maxdepth: 2
    :caption: The Pipeline

    details/pipeline
    details/configuration





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