Skip to content

NGS: Software Suites

Ensembl-API

GCATemplates available: no

The Ensembl API is available in the EnsEMBLCoreAPI module:

module spider EnsEMBLCoreAPI

See the Ensembl Core API Tutorial for usage.

EMBOSS

GCATemplates available: no

module spider EMBOSS

EMBOSS homepage

UCSCtools

GCATemplates available: no

List of tools and usages found here

module spider UCSCtools

GCATemplates available: no

PLINK homepage

module spider PLINK

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

Plink v1.9 is still beta and being updated frequently so it is best not to add to the HPRC clusters as a module.

There is a precompiled Linux 64-bit (Stable (beta 6.8, 15 Feb) or newer) binary version available that you can download and add to your $PATH.

Version 1.9 will change frequently since it is still beta so you should review your results files and check their website and download the latest version as needed.

Gemini

GCATemplates available: no

Gemini homepage

module spider Gemini

GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome.

Gemini Data is saved here:

/scratch/data/bio/Gemini/gemini_data