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454 Tools on Biowulf & Helix

Description

The GS Data Analysis Software package includes the tools to investigate complex genomic variation in samples including de novo assembly, reference guided alignment and variant calling. It includes gsAssembler (de novo assembler), gsMapper (reference mapper), and gsAmplicon (amplicon variant analyzer).

Web sites

Running Roche 454 GUI tools on Helix

The three tools (gsAssembler, gsMapper, and gsAmplicon are GUI tools. This means that you have to have to have X windows running on your computer and connect to helix using the proper ssh paramaters for forwarding the X windows data from helix to your local machine:

ssh -XC helix.nih.gov

Then load the module and start the desired application:

$ module load roche454/2.9
$ gsAssembler

Since the GUI applications run their processing steps on the node they were started on, it is prererable to run them on interactive compute nodes (see below).

Running an interactive job on Biowulf

Start an interactive node

$ sinteractive --x11

On the interactive node, load the module and start the application

$ module load roche454/2.9
$ gsAssembler