FastQC v0.11.1 is the first release for a long time and is a major update to the package. This release adds some significant new features to the program which will hopefully make it more useful.

The major new features in this release are:

• Added configurable warn/fail thresholds for all modules
• Allow modules to be selectively turned off
• Added a per-tile quality plot for Illumina libraries
• Added an adapter content plot
• Improved the duplication plot
• Improved the Kmer module
• Used embedded graphics in the HTML output so you can distribute a single file
• Added the ability to read data from stdin
• Changed how base grouping works to better accommodate long reads
• Dropped support for Solexa64 format (NB not Phred 64 which is still supported)

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