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:

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

Documentation

Setup

• Install
• Usage
• Execution of Atlas

The Pipeline

• The Atlas pipeline
• Expected output
  • Quality control
  • Assembly
  • Genomes
  • Gene Catalog
• Configure Atlas
  • Example config file
  • Remove reads from Host
  • Detailed configuration