STACKS

Overview

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.

Versions 1.48 and 2.0 Beta9 are installed on the CSF.

Restrictions on use

There are no restrictions on accessing this software on the CSF. It is released under the GNU GPLv3 license and all usage should fall within that license.

Please cite your usage of this software using the details provided in the STACKS citation section of their website.

Set up procedure

To access the software you must first load the modulefile:

module load apps/gcc/stacks/1.48             # Last release of the version 1 app
module load apps/gcc/stacks/2.0Beta9         # Development release of the version 2 app

Note that some of the data file formats read and written by the applications have changed between version 1 and version 2. Hence you may have problems reading files in to tools in version 2 that were originally generated in version 1. You should consult the version 1 manual and the version 2 manual for the sections which describe the fields written to the output files by the various tools.

Running the application

Please do not run STACKS executables on the login node. Jobs should be submitted to the compute nodes via batch. The following executables are available:

# Executables (please check command-line flags to specify number of threads (cores))
clone_filter  kmer_filter   process_radtags     stacks-dist-extract          tsv2bam
cstacks       phasedstacks  process_shortreads  stacks-gdb                   ustacks
gstacks       populations   sstacks             stacks-integrate-alignments

# Python scripts
integrate_alignments.py
count_fixed_catalog_snps.py

# Perl scripts
denovo_map.pl
ref_map.pl

If you wish to determine the command-line flags accepted by an executable you may run it on the login node with the --help flag added. For example:

ustacks --help

Note that you must check what flag is required to specify the number of threads (cores) to use.

Serial batch job submission

Make sure you have the modulefile loaded then create a batch submission script, for example:

#!/bin/bash
#$ -cwd             # Job will run from the current directory
#$ -V               # Job will inherit current environment settings

# Example using the ustacks executable
ustacks -f file_path -i id -o path   -M max_dist -m min_cov
                                     #
                                     # Optional args 

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Parallel batch job submission

Please note that some of the STACKS executables use -t numcores to enable parallelism with the specified number of cores, and some of the apps use -p numcores to enable the parallelism. You must check which flag is used and specify this correctly in your jobscript.

Make sure you have the modulefile loaded then create a batch submission script, for example:

#!/bin/bash
#$ -cwd             # Job will run from the current directory
#$ -V               # Job will inherit current environment settings
#$ -pe smp.pe 8     # Number of cores (2-24 permitted)

# Example using the ustacks executable.
# $NSLOTS is automatically set to the number of cores requested above.
# We use this to inform the application of the number of cores to use.

# Example using the ustacks executable
ustacks -f file_path -i id -o path -p $NSLOTS   -M max_dist -m min_cov
                                                #
                                                # Optional args

# Example using the populations executable
populations -P dir -t $NSLOTS

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Further info

• STACKS v1 online manual
• STACKS v2 online manual

Updates

None.