BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.
RQCFilter2 is a revised version of RQCFilter that uses a common path for all dependencies. The dependencies are available at http://portal.nersc.gov/dna/microbial/assembly/bushnell/RQCFilterData.tar
Performs quality-trimming, artifact removal, linker-trimming, adapter trimming, and spike-in removal using BBDuk. Performs human/cat/dog/mouse/microbe removal using BBMap. It requires 40 GB RAM for mousecatdoghuman, but only 1GB or so without them.
Usage: rqcfilter2.sh in='' path='' rqcfilterdata=''