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Stacks2: cstacks (version 2.55+galaxy4)
output from previous Stacks pipeline steps e.g. denovo_map, refmap or ustacks
If set, the catalog will be built from samples listed in this file
(default 1; suggested: set to ustacks -M)
default: automatic

What it does

A catalog can be built from any set of samples processed by ustacks. It will create a set of consensus loci, merging alleles together. In the case of a genetic cross, a catalog would be constructed from the parents of the cross to create a set of all possible alleles expected in the progeny of the cross.

Input files

Output from denovo_map or ustacks

Output files

See Stacks output description

Notes: For the tags file, each stack will start in the file with a consensus sequence for the entire stack followed by the flags for that stack. Then, each individual read that was merged into that stack will follow. The next stack will start with another consensus sequence.

See Stacks output description

Notes: If a stack has two SNPs called within it, then there will be two lines in this file listing each one.

See Stacks output description

Created by:

Stacks was developed by Julian Catchen with contributions from Angel Amores, Paul Hohenlohe, and Bill Cresko

Project links:

Stacks website

Stacks manual

Stacks google group