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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.

Stacks is available as a module on Apocrita.

Usage

To run the default installed version of Stacks, simply load the stacks module:

$ module load stacks
Usage: <command> [options] [--help] [--version]

The following commands are available:

process_radtags      Examines raw reads from an Illumina sequencing run and
first, checks that the barcode and the RAD cutsite are intact, and
demultiplexes the data.

process_shortreads   Performs the same task as process_radtags for fast
cleaning of randomly sheared genomic or transcriptomic data, not for RAD data.

clone_filter         Designed to identify PCR clones.

kmer_filter          Allows paired or single-end reads to be filtered according
 to the number or rare or abundant kmers they contain.

ustacks              Takes as input a set of short-read sequences and aligns
them into exactly-matching stacks (or putative alleles).

cstacks              Builds a catalog from any set of samples processed by the
ustacks or pstacks programs.

sstacks              Sets of stacks, i.e. putative loci, constructed by the
ustacks program can be searched against a catalog produced by cstacks.

tsv2bam              Transpose data so that it is oriented by locus, instead
of by sample.

gstacks              Examines a RAD data set one locus at a time, looking at
all individuals in the metapopulation for that locus.

populations          Analyze a population of individual samples computing a
number of population genetics statistics as well as exporting a variety of
standard output formats.

The following scripts are included in the Stacks package and allows preset pipelines to be run:

denovo_map.pl
ref_map.pl

For full usage documentation, run <command> -h.

Example job

Serial job

The simplest way to execute the entire Stacks pipeline is to run it via the denovo_map.pl program.

Here is an example job running on 2 cores and 8G memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 2
#$ -l h_rt=1:0:0
#$ -l h_vmem=4G

module load stacks

denovo_map.pl -T ${NSLOTS} -M 4 -n 4 -o ./stacks/ \
              --samples ./samples --popmap ./popmaps/popmap

References