Using Bioinformatics Tools (Blast, BWA, etc.)

Audience: Faculty, Researchers and Staff

This KB Article References:
This Information is Intended for: Faculty, Researchers, Staff
Last Updated: January 18, 2018

A variety of widely used tools for bioinformatics analysis have been installed on Seawulf.  Many of these programs were installed using Anaconda 2, including:

ABySS
Augustus
Bamtools
BEAST2
Bedtools
Blast+
Bowtie2
BWA
Canu
Cd-hit
Clustalw
Cufflinks
Cutadapt
EMBOSS
FastQC
HISAT2
Hmmer
Kallisto
MAFFT
Mothur
MrBayes
MUSCLE
PAML
Picard
RAxML
RepeatMasker
RepeatModeler
RSEM
Samtools
SNAP
SnpEff
SPAdes
STAR
T-Coffee
Tophat
Transdecoder
Trimmomatic
Trinity
VCFTools
Velvet 

To access any of these programs load the following modules:

module load shared
module load anaconda/2

Once the module is loaded, the binaries for the above programs  will be available in your path.  

Some additional bioinformatics tools have been installed with their own separate modules.  These include:

GATK/4.0.0
revbayes/1.06

After loading their respective modules, GATK can be invoked by typing "gatk", while RevBayes can be accessed with "rb".

For further instructions on how to run individual programs, please consult the relevant online documentation.

When running a program, you will need to execute it as part of PBS bash script.  An example PBS script for running Trinity RNA-seq assembly can be found at: 

/gpfs/projects/samples/Trinity/

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