FASTQ tools

Here are my favorite FASTQ processing utils:

FASTQC:

To run a QC on your data.

http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/

To run in batch mode with zipped output:

java* -Xmx250m -cp <> uk.ac.bbsrc.babraham.FastQC.FastQCApplication <>

*: make sure that java is at least version 1.6

FASTX Toolkit:

Bunch of scripts for processing the fastq files and qc, but fastqc is better for qc'ing.

http://hannonlab.cshl.edu/fastx_toolkit/download.html