Dynamic quality trimming for raw FASTQ input data

Exciting news! PhyloSift now supports dynamic quality trimming of raw FASTQ data. Upon detecting FASTQ input files, the software workflow will perform Heng Li’s BWA quality trim algorithm (when running PhyloSift all or search mode). Reads are trimmed according to the following formula (where l is the original read length):

argmax_x{\sum_{i=x+1}^l(INT-q_i)} if q_l<INT

To utilize this new feature, download the development version of PhyloSift, available at http://edhar.genomecenter.ucdavis.edu/~koadman/phylosift/devel/phylosift_latest.tar.bz2