Stacks

sstacks

Sets of stacks, i.e. putative loci, constructed by the ustacks or pstacks programs 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 [--aligned] -P dir [-b batch_id] -M popmap [-p n_threads]
sstacks [--aligned] -c catalog_path -s sample_path [-s sample_path ...] -o path [-p n_threads]

Gapped assembly options:

Example Usage

Match each of three samples of progeny from a genetic map against the catalog, one at a time:

% sstacks -b 1 -c ./stacks/batch_1 -s ./stacks/progeny_01 -p 15 % sstacks -b 1 -c ./stacks/batch_1 -s ./stacks/progeny_02 -p 15 % sstacks -b 1 -c ./stacks/batch_1 -s ./stacks/progeny_03 -p 15

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 -b 1 -c ./stacks/batch_1 -s ./stacks/sample_01 -s ./stacks/sample_02 -s ./stacks/sample_03 -p 15

Specify a directory containing all of the Stacks files generated with ustacks or pstacks, 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 here for information on population maps).

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

Other Pipeline Programs

Raw Reads

Core

Execution control

Utilities