A workflow for metagenomic projects
A snakemake workflow for paired- and/or single-end whole-genome shotgun metagenomic data.
You can use this workflow for e.g.:
- read-trimming and QC
- taxonomic classification
- assembly
- functional and taxonomic annotation
- metagenomic binning
See the Wiki-pages for instructions on how to run the workflow.
- Checkout the latest version:
git clone https://github.com/NBISweden/nbis-meta.git
or download a tarball of the latest release from the release page.
- Install and activate the workflow environment:
conda env create -f environment.yml
conda activate nbis-meta
To pull the latest Docker image with all dependencies and source code from DockerHub, run:
docker pull nbisweden/nbis-metaSee the Wiki for instructions on how to run the Workflow with Docker.