---
tags:
  - Free
catalog:
  name: Stacks
  description: Pipeline for building loci from short-read sequences (e.g. RAD-seq data)
  license_type: Free
  disciplines:
    - Biosciences
  available_on:
    - Puhti
---

# Stacks

Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the 
Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for 
the purpose of building genetic maps and conducting population genomics and phylogeography.

[TOC]

## License

Free to use and open source under [GNU GPLv3](https://www.gnu.org/licenses/gpl-3.0.html).

## Available

* Puhti: 2.62, 2.65

## Usage

The command-line tools of the Stacks package are installed on Puhti. To set up the most recent stacks environment on Puhti, 
run the command:

```bash
module load biokit
```

After that you can launch Stacks commands like `denovo_map.pl`. For example:

```bash
denovo_map.pl -m 3 -M 2 -n 3 -T 4 -S -b 1 -t -a 2010-11-30 -o ./stacks -p ./samples/male.fa -p ./samples/female.fa -r ./samples/progeny_1.fa -r ./samples/progeny_2.fa -r ./samples/progeny_3.fa
```

As stacks jobs can be rather heavy, they should be executed as batch jobs. The Stacks installation on Puhti is not linked to 
a stacks result database and web interface. Because of that you should use option `-S` (and not options `-B` and `-D`) in 
`denovo_map.pl` runs.

It is, however, possible to set up your own Stacks database and WWW interface to a virtual machine running in the 
cPouta cloud environment of CSC. [See more details here](../cloud/pouta/launch-vm-from-web-gui.md).

## More information

* [Stacks home page](https://catchenlab.life.illinois.edu/stacks/)
* [Setting up a Stacks server in cPouta](../cloud/pouta/launch-vm-from-web-gui.md)
