The CGAT code collection has grown out of the work in comparative genomics by the Ponting group in the last decade. Now, CGAT has added functionality to do next-generation sequencing analysis.
The CGAT Code collection has two components. The first component is a collection of scripts, the CGAT tools. The second component is a collection of pipelines.
CGAT uses environment modules. Type
module load CGAT
Create a PBS batch script cgat.sh:
Then submit the job:
$ qsub -l nodes=1:c16 cgat.sh
- Type "cgat --help" at the prompt
- CGAT Documentation