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

Full documentation is hosted on autometa.readthedocs.io

conda install -c bioconda autometa

conda create -n autometa -c bioconda autometa

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

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

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

nf-core launch KwanLab/Autometa

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: