reaper v13.274 (A program for demultiplexing, trimming and filtering short read sequencing data)
Reaper is a fast and highly memory-efficient program written in C, able to process 60-200M reads per hour. It allows tunable identification and stripping of adapter sequences using Smith-Waterman alignments, recognises several types of barcode position and read layout, demultiplexes barcodes, and generates extensive summary statistics including base call quality and tri-nucleotide complexity scores that can be used to perform quality control. Users can specify their own input and output formats in a simple specification language. By default Reaper expects FASTQ input, that may have been compressed. Reaper has been designed to address complex experimental designs and allow filtering based on a range of parameters within a single iteration of the software with minimal impact on speed and memory requirements. Reaper is shipped with tally, a program for uniquifying reads that is optimised to minimise memory usage by compressing sequences in memory.