---
tags:
  - Free
catalog:
  name: Chipster_genomes
  description: Tool to download aligner indexes used by Chipster to Puhti
  license_type: Free
  disciplines:
    - Biosciences
  available_on:
    - Puhti
---

# Chipster_genomes

Chipster_genomes is a help tool to download genome indexes used in [Chipster software](https://chipster.csc.fi/index.shtml) to Puhti.
CSC is maintaining several short read aligners (e.g. BWA, Bowtie2, STAR) in Puhti, but not the pre-calculated 
indexes for reference genomes. By default, users need to import and index themselves the reference genomes they are using.

The Chipster server, however, contains indexes for a set of commonly used reference organisms for several aligners.

The genome data and indexes used in Chipster are based on the data available in Ensembl and Ensembl genomes databases. 
However, in Chipster, only those sequences (chromosomes) that have been assigned to a karyotype, are included. 
Further, in GTF files negative location values are removed.

Thus, the data downloaded from Chipster server may, in some cases, differ from the data obtained directly from Ensembl.

[TOC]

## License

Free to use and open source.
 
## Available

Available in Puhti.

## Usage

The `chipster_genomes` tool is included in the `biokit` module, so to make it available, you must first run the set-up command:

```bash
module load biokit
```

After that, you can use `chipster_genomes` command. This command needs two parameters:

* File or index type (bed, gtf, fasta, bowtie, bowtie2, BWA, Hisat2, TopHat2)
* Species name

If the command is launched without any arguments, it first lists the available data types and asks to select one of them.
Then the species available for the given datatype are listed, and the tool asks the user to select one of them.

```bash
chipster_genomes
```

The data type can, alternatively, be given as the first argument and the species name as the second argument.
For example, the BWA indexes of Danio_rerio.GRCz11 can be retrieved with the command:

```bash
chipster_genomes bwa Danio_rerio.GRCz11
```

Note that as the index files may be rather large, you should normally download the data to your `/scratch` disk area.
