# Welcome to MeSS !

[![](https://img.shields.io/static/v1?label=CLI&message=Snaketool&color=blueviolet)](https://github.com/beardymcjohnface/Snaketool)
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
[![version](https://img.shields.io/conda/v/bioconda/mess?label=version&color=blue)](http://bioconda.github.io/recipes/mess/README.html)
[![downloads](https://img.shields.io/conda/dn/bioconda/mess.svg)](https://anaconda.org/bioconda/mess)
[![tests](https://github.com/metagenlab/MeSS/actions/workflows/unit-tests.yml/badge.svg)](https://github.com/metagenlab/MeSS/actions/workflows/unit-tests.yml)
[![docs](https://github.com/metagenlab/MeSS/actions/workflows/build-docs.yml/badge.svg)](https://github.com/metagenlab/MeSS/actions/workflows/build-docs.yml)

The Metagenomic Sequence Simulator (MeSS) is a [Snakemake](https://github.com/snakemake/snakemake) pipeline, implemented using [Snaketool](https://github.com/beardymcjohnface/Snaketool), for simulating illumina, Oxford Nanopore (ONT) and Pacific Bioscience (PacBio) shotgun metagenomic samples.

## Overview

MeSS takes as input NCBI taxa or local genome assemblies to generate either long (PacBio or ONT) or short (illumina) reads. In addition to reads, MeSS optionally generates bam alignment files and taxonomic profiles in [bioboxes format](https://github.com/bioboxes/rfc).

![overview](docs/images/workflow.svg)

## Installation

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/mess/README.html)

```sh
mamba create -n mess mess
```

## Usage

![`mess -h`](docs/images/mess-help.svg)
