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Stacks2: de novo map (version 2.55+galaxy4)
Assembly options
Assembly options 0
SNP model options
SNP model options 0
Paired-end options
Paired-end options 0
Population filtering options
Population filtering options 0

What it does

This program will run each of the Stacks components: first, running ustacks on each of the samples specified, building loci and calling SNPs in each. Second, cstacks will be run to create a catalog of all loci that were marked as 'parents' or 'samples' on the command line, and finally, sstacks will be executed to match each sample against the catalog. A bit more detail on this process can be found in the FAQ. The denovo_map.pl program will also load the results of each stage of the analysis: individual loci, the catalog, and matches against the catalog into the database (although this can be disabled). After matching, the program will build a database index to speed up access (index_radtags.pl) and enable web-based filtering.


Input files

FASTQ, FASTA

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

See Stacks output description

Notes: Each line in this file records a match between a catalog locus and a locus in an individual, for a particular haplotype. The Batch ID plus the Catalog ID together represent a unique locus in the entire population, while the Sample ID and the Stack ID together represent a unique locus in an individual sample.

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