FastQCmod is an extension to the great FastQC (currently build on release v0.10.1).
The extension includes a logic to extract the analysis results of the
FastQC analysis methods and write a more computer readable output,
to allow for a simplified reusal by e.g. RawReadManipulator.
Furtheron, in the light of the fact that CPU power is currently more
than I/O-Bandwidth, FastQCmod contains code for parallelization of the
of single fastq-files, compared to the per-sample/per-file
parallelization of the original
FastQC. A backport of recent FastQC versions to FastQCmod is in preparation.
The source-code of FastQCmod (based on FastQC v0.10.1) is available
under the GPLv3 license.
The RawReadManipulator (RRM) is an in-house development of a modular, highly
parallelized filtering pipeline for raw reads.
The java application is easily extensible with new or custom
filtering-modules as necessary,
and makes use of the data-independence that reads (or read-pairs) have
towards each other.
All available filters have many available configuration options, such
that the most common filtering
needs should be met when using RRM.
Tests have shown the parallelization to be scaling well with the number
of CPUs given to the task,
with the bottleneck of available data-I/O-bandwith as the limiting
factor in terms of filtering-speed.