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stacks website  

Stacks is a software pipeline for building loci out of a set of short-read sequenced samples. Stacks was developed for the purpose of building genetic maps from RAD-Tag Illumina sequence data, but can also be readily applied to population studies, and phylogeography.

Required Modules

modules documentation


  • stacks

System Variables

  • HPC_{{#uppercase:stacks}}_DIR - installation directory

Additional Information

The command line pipeline is available via the "stacks" module.

The web interface that can be used for visualizing genetic maps and correcting the analysis is being installed and tested as of Aug 21st, 2012.

To run stacks with database export:

  • Log into a test node and load the stacks module:
  • Create a database with a name that starts with "stacks_${USER}_" or "radtags_${USER}_" using the 'hpc_create_stacks_db' script

For example:

hpc_create_stacks_db "stacks_${USER}_mytest1"

The $USER variable will be expaned to your username. This will help us determine who a database belongs to if there is an issue or when we're cleaning up the old databases. Make sure to use the double quotes. Of course, you can explicitly provide a database name like

hpc_create_stacks_db stacks_jdoe_project21

The script will produce an error and quit if the database already exists.

Use the 'hpc_list_stacks_databases [keyword]' command with or without a search keyword. If there is no keyword the command will list all stacks databases. If a search keyword is provided the command will list only databases containing that keyword in their name.

For example:

hpc_list_stacks_databases test

To delete a stacks database use the 'hpc_remove_stacks_database [database]' command and provide the name of the database you want to delete as an argument.

  • Log out of the dev node.
  • Run '' as usual via a batch job specifying the database name with "-B test1_radtags".
  • Browse to and use your HPC credentials to log in and view the results. The exact URI is constructed as follows:

Substitute your own database name for 'DATABASE' at the end of the URI. To see an example view - go to for the output of a Stacks Tutorial.