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Stacks2: cstacks (version 2.55+galaxy4)

Loci and polymorphism:

output from previous Stacks pipeline steps e.g. denovo_map, refmap or ustacks

Population map:

If set, the catalog will be built from samples listed in this file

Number of mismatches allowed between sample loci when building the catalog:

(default 1; suggested: set to ustacks -M)

Perform gapped alignments between stacks:

Number of gaps allowed between stacks before merging:

Minimum length of aligned sequence in a gapped alignment:

K-mer size for matching between between catalog loci:

default: automatic

Report query loci that match more than one catalog locus:

Add log output as dataset:

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

catalog.tags file:

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.

catalog.snps file:

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.

catalog.alleles file:

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