cgatools on Helix
cgatools provides tools for downstream analysis of Complete Genomics data. The focus is to provide command line utilities. The general areas of functionality include genome comparison, format conversion, and reference tools.
The easiest way to add the cgatools utilities to your environment is by using the 'module load cgatools' command, as in the example below.
Sample session
Example files can be downloaded from ftp://ftp2.completegenomics.com/. The reference files can be downloaded from ftp://ftp.completegenomics.com/ReferenceFiles/
Add the cgatools executables to your path:
$ module load cgatools
Convert reference sequence from fasta format to crr format:
$ cgatools fasta2crr --input build36.fa.bz2 --output build36.crr
List the reference:
$ cgatools listcrr --reference build36.crr --output listcrr.out
