Sets of stacks, i.e. putative loci, constructed by the ustacks program can be searched against a catalog produced by cstacks. In the case of a genetic map, stacks from the progeny would be matched against the catalog to determine which progeny contain which parental alleles. In the case of a general population, all samples in the population would be matched against the catalog with sstacks.

Program Options

sstacks -P dir -M popmap [-p n_threads]
sstacks -c catalog_path -s sample_path [-s sample_path ...] -o path [-p n_threads]

Gapped assembly options:

Example Usage

  1. Specify a directory containing all of the Stacks files generated with ustacks and cstacks. Then specify the path to a population map that contains all of the samples you would like to match against the catalog (see the manual for information on population maps).

    % sstacks -P ./stacks -M ./popmap -p 8

  2. Match each of three samples from a population against the catalog, one at a time:

    % sstacks -c ./stacks/catalog -s ./stacks/sample_01 -p 15 % sstacks -c ./stacks/catalog -s ./stacks/sample_02 -p 15 % sstacks -c ./stacks/catalog -s ./stacks/sample_03 -p 15

    This preceeding case is particularly useful when a large number of samples require processing. In this case, if you have access to a queued cluster, you can specify the sstacks run for each sample separately.

  3. Match each of three samples in a population against the catalog in a single command (saving the time of having to reload the catalog each exectution):

    % sstacks -c ./stacks/catalog -s ./stacks/sample_01 -s ./stacks/sample_02 -s ./stacks/sample_03 -p 15

    This case is identical to the first example, except without using a population map. It can be used on a single computational node.

Other Pipeline Programs

Raw Reads


Execution control