FASTQC

This java app reads a fastq file and generated various quality metrics.

It can be run from both the command-line or a GUI. It is also pretty fast - processing over 4M reads in under 8 seconds - but I ran it on a beast of a machine with 256 GB of RAM.

It is available for download from this site:

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

Here is the command-line:
/usr/local/bin/java-1.6.0 -Xmx250m -cp /usr/local/devel/BCIS/external_software/FastQC uk.ac.bbsrc.babraham.FastQC.FastQCApplication < input.fastq >

Where the text in blue represents the installation location.

The output will be a set of HTML and image files zipped inside a folder named < input >_fastqc.