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Stacks2: tsv2bam (version 2.55+galaxy4)

Loci and polymorphism:

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

Catalog of loci:

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

Matches to the catalog:

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

Short read data from individuals:

Paired end data or reverse reads. If a paired list is provided only the reverse reads are used in tsv2bam. Leave selection empty if you analyse single end data.

Reads:

Population map:

If set, matching will be done only for samples listed in this file

Add log output as dataset:

What it does

The unique stacks program will take as input a set of short-read sequences and align them into exactly-matching stacks. Comparing the stacks it will form a set of loci and detect SNPs at each locus using a maximum likelihood framework

Input files

FASTQ, FASTA

Output files

XXX.tags.tsv 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.

XXX.snps.tsv 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.

XXX.alleles.tsv 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