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 individual 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 widely available than I/O-Bandwidth, FastQCmod contains code for parallelization of the analysis 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.