Bioinformatics Software

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Software installed in Bioinformatics cluster

PEAKachu

Peak calling tool for CLIP-seq data

Github

To use run this command

module load peakachu


STAR

Ultrafast universal RNA-seq aligner

Github

Installed version: 2.7.3a


Bedtools

Bedtools is a fast, flexible toolset for genome arithmetic.

Webpage

Installed version: 2.29.0

Usage:

module load bedtools

GATK

Genome Analysis Toolkit. It is a collection of command-line tools for analyzing high-throughput sequencing data with a primary focus on variant discovery.

The tools can be used individually or chained together into complete workflows.

Webpage

Installed version: 4.1.3.0

Usage:

module load gatk

SourceTracker2

SourceTracker is a Bayesian approach to estimate the proportion of contaminants in a given community that come from possible source environments.

Webpage

Usage:

module load conda-st2