Hi All,

I'm new to NGS analysis, and command line analysis for that matter. (I'm in the process of learning perl/python - so please bear with this newbie query).
I've installed the fastx-toolkit and the scripts here are working great, but couldn't find the fastq_groomer script anywhere on the galaxy page, at http://hannonlab.cshl.edu/fastx_toolkit/index.html, nor on the web, except from this page: http://bitbucket.org/galaxy/galaxy-dist/src/tip/tools/fastq/

I tried running it via: python fastq_groomer.py input_file input_type output_type
as per the fastq_groomer.xml, but doesn't work.

Is this the correct fastq_groomer script, am I running it correctly, or where can I get this script to run like the other fastx-toolkit scripts?
I know I could use the Galaxy server/ or install galaxy locally, but for several reasons at the moment want to use the individual scripts.

Thanks in advance!

Ken

Kenlee Nakasugi
School of Molecular Bioscience
University of Sydney