It is designed to take as input several fastq files (PE as well as single) and process them efficiently (memory usage and execution time).
Inside ROCK, reads are filtered by a count min sketch.
What makes ROCK different from other read filtering tools is that reads are processed by decreasing order of quality scores. Ie reads with the highest quality score are sure to be selected by the filter and those with low quality score have more chances to be discarded.
ROCK provides different options for parameterizing the count min sketch. They are detailed in the man documentation.
ROCK compiles with gcc 4.4.7 and clang 503.0.40.
It has been tested under OS X 10.9 and linux CentOS 6.7 and should run on other systems of the unix family.
For distribuability reasons, choice has been made to develop in C++ 98 and make ROCK compatible with C++ 11.
You can compile/install ROCK by rectly running configure :
./configure
make check
make
make install
Any remark/suggestion/problem should be reported to <vlegrand@pasteur.fr>.
