Illumina, Inc.

Stacks Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. Pipeline components The Stacks pipeline is designed modularly to perform several different types of analyses. The process_radtags program examines raw reads from an Illumina sequencing run and first, checks that the barcode and the restriction enzyme cutsite are intact (correcting minor errors). The process_shortreads program performs the same task as process_radtags for fast cleaning of randomly sheared genomic or transcriptomic data. The clone_filter program will take a set of paired-end reads and reduce them according to PCR clones (a PCR clone is a pair of reads that match exactly, while paried-end reads from two different DNA molecules will nearly always be slightly different lengths).