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. Programs listed under Raw Reads are used to clean and filter raw sequence data. Programs under Core represent the main Stacks pipeline -- building loci (ustacks or pstacks), creating a catalog of loci (cstacks, and matching samples back against the catalog (sstacks), followed by assignment of genotypes (genetic mapping) or population genomics analysis.
Programs under Execution Control will run the whole pipeline, followed by a number of Utility programs for things such as building paired-end contigs. A catalog can be built from any set of samples processed by the ustacks program. Novell GroupWise. FuseMail Portal. Illumina, Inc. Paychex. Fluidigm FTP. Tracking - Shipping - Freight - Delivery Services.