Galaxy | Tool Preview

STACKS : De novo map (version 1.0.0)
FASTQ/FASTA/ZIP/TAR.GZ files containing parent sequences from a mapping cross
be careful, all files must have a paired-end friend
FASTQ/FASTA/ZIP/TAR.GZ files containing progeny sequences from a mapping cross
advanced_options 0
SNP_Model_Options 0
please see below for details

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 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 ( and enable web-based filtering.

Created by:

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


Input files:

FASTQ, FASTA, zip, tar.gz

Output files:

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.

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

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.

Instructions to add the functionality of archives management in Galaxy on the eBiogenouest HUB wiki .

Output type:

Project links:

STACKS website .

STACKS manual .

STACKS google group .


-J. Catchen, P. Hohenlohe, S. Bassham, A. Amores, and W. Cresko. Stacks: an analysis tool set for population genomics. Molecular Ecology. 2013.

-J. Catchen, S. Bassham, T. Wilson, M. Currey, C. O'Brien, Q. Yeates, and W. Cresko. The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing. Molecular Ecology. 2013.

-J. Catchen, A. Amores, P. Hohenlohe, W. Cresko, and J. Postlethwait. Stacks: building and genotyping loci de novo from short-read sequences. G3: Genes, Genomes, Genetics, 1:171-182, 2011.

-A. Amores, J. Catchen, A. Ferrara, Q. Fontenot and J. Postlethwait. Genome evolution and meiotic maps by massively parallel DNA sequencing: Spotted gar, an outgroup for the teleost genome duplication. Genetics, 188:799'808, 2011.

-P. Hohenlohe, S. Amish, J. Catchen, F. Allendorf, G. Luikart. RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow trout and westslope cutthroat trout. Molecular Ecology Resources, 11(s1):117-122, 2011.

-K. Emerson, C. Merz, J. Catchen, P. Hohenlohe, W. Cresko, W. Bradshaw, C. Holzapfel. Resolving postglacial phylogeography using high-throughput sequencing. Proceedings of the National Academy of Science, 107(37):16196-200, 2010.

Integrated by:

Yvan Le Bras and Cyril Monjeaud

GenOuest Bio-informatics Core Facility

UMR 6074 IRISA INRIA-CNRS-UR1 Rennes (France)