Autometa

An automated binning pipeline for single metagenomes, in particular host-associated and highly complex ones. Autometa is copyright 2020 Ian J. Miller, Evan Rees, Izaak Miller and Jason C. Kwan, and is released under the GNU Affero General Public License v3 (see LICENSE.txt). If you find Autometa useful to your work, please cite:

Miller, I. J.; Rees, E. R.; Ross, J.; Miller, I.; Baxa, J.; Lopera, J.; Kerby, R. L.; Rey, F. E.; Kwan, J. C. Autometa: Automated extraction of microbial genomes from individual shotgun metagenomes. Nucleic Acids Research, 2019. DOI: https://doi.org/10.1093/nar/gkz148

Documentation

Full documentation is hosted on autometa.readthedocs.io

Quickstart

🐚 Bash workflow

1. Setup env

Install into your current env...

mamba install -c conda-forge -c bioconda autometa

... or create a new env

mamba create -n autometa -c conda-forge -c bioconda autometa

2. Download the bash workflow template, autometa.sh

3. Edit the input parameters

4. Run the workflow

🍏 Nextflow Workflow

1. Setup env

🧑‍🎓 This workflow requires only nextflow and nf-core be installed.

Install into your current env...

mamba env update -n <your-env> --file=https://raw.githubusercontent.com/KwanLab/Autometa/main/nextflow-env.yml

... or create a new env

mamba env create --file=https://raw.githubusercontent.com/KwanLab/Autometa/main/nextflow-env.yml
# Activate the env after creation
mamba activate autometa-nf

2. Launch and run the workflow

nf-core launch KwanLab/Autometa

For developers

---

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x. In addition, references of tools and data used in this pipeline are as follows: