# nf-core/coproid: Documentation

![logo](source/_static/img/coproid_logo_small.jpg) ![nf-core-logo](../assets/img/coproID_nf-core_logo_small.png)

**coproID** (**CO**prolite **ID**entification) is a tool developed at the
[Max Planck insitute for the Science of Human History](http://www.shh.mpg.de/en)
by [Maxime Borry](https://github.com/maxibor)

The purpose of **coproID** is to help identify the host of given sequenced
microbiome when there is a doubt between species.

**coproID** is a pipeline developed using [Nextflow](https://www.nextflow.io/)

and made available through [nf-core](https://github.com/nf-core)

Even though it was developed with coprolite host identification in mind, it can
 be applied to any microbiome, provided they contain host DNA.

1.  [Installation](https://nf-co.re/usage/installation)
2.  Pipeline configuration
    -   [Local installation](https://nf-co.re/usage/local_installation)
    -   [Adding your own system config](https://nf-co.re/usage/adding_own_config)
    -   [Reference genomes](https://nf-co.re/usage/reference_genomes)
3.  [Running the pipeline](usage.md)
4.  [Output and how to interpret the results](output.md)
5.  [Troubleshooting](https://nf-co.re/usage/troubleshooting)

## Quick start

Example:

    nextflow run maxibor/coproid --genome1 'GRCh37' --genome2 'CanFam3.1' --name1 'Homo_sapiens' --name2 'Canis_familiaris' --reads '*_R{1,2}.fastq.gz'

## coproID example workFlow

![dag](source/_static/img/coproid_dag.png)

## How to cite coproID

The coproID article is coming.
