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A snakemake workflow for metagenomic projects

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# NBIS-Metagenomics
A workflow for metagenomic projects

[![Python 3.7](https://img.shields.io/badge/python-≥3.7-brightgreen.svg)](https://www.python.org/downloads/release/python-37/)
[![Snakemake 5.18](https://img.shields.io/badge/snakemake->5.18-brightgreen.svg)](https://img.shields.io/badge/snakemake-5.11.2)
![CI](https://github.com/NBISweden/nbis-meta/workflows/CI/badge.svg?branch=main)
![Docker](https://img.shields.io/docker/pulls/nbisweden/nbis-meta)
[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)

## Overview
A [snakemake](http://snakemake.readthedocs.io/en/stable/) 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](https://github.com/NBISweden/nbis-meta/wiki) for
instructions on how to run the workflow.

## Installation

### From GitHub
1. 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](https://github.com/NBISweden/nbis-meta/releases).

2. Install and activate the workflow environment:

```
conda env create -f environment.yml
conda activate nbis-meta
```

### From DockerHub

To pull the latest Docker image with all dependencies and source code from
DockerHub, run:

```bash
docker pull nbisweden/nbis-meta
```

See the Wiki for instructions on how to run the Workflow with Docker.

nbis-meta

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