- ustacks - 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.
- pstacks - Similar to ustacks, except this program will extract stacks
that have been aligned to a reference genome by a program such as
Bowtie or GSnap and identify SNPs. These
stacks can then be processed with cstacks or sstacks.
- cstacks - A catalog can be built from any set of samples processed
by the ustacks program. 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.
- sstacks - Sets of stacks constructed by the ustacks program can be
searched against a catalog produced by the cstacks program. In the case of a genetic map, stacks
from the progeny would be matched against the catalog to determine which progeny contain which
- genotypes - exports Stacks data as a set of observed haplotypes, or with the haplotypes
encoded into genotypes, in either a generic format or for a particular program such as JoinMap or R/QTL. It also provides
methods for making automated corrections to certain types of loci.
- populations - This program will be executed in place of the exisiting genotypes
program when a population is being processed through the pipeline. The populations program will output site level SNP calls (in VCF format)
and will compute summary statistics such as Pi, Fis, and Fst.
- process_radtags - examines raw reads from an Illumina sequencing run and first,
checks that the barcode and the RAD cutsite are intact (correcting minor errors). Second, it slides a window down
the length of the read and checks the average quality score within the window. If the score drops below 90%
probability of being correct, the read is discarded.
- process_shortreads - performs the same task as process_radtags for fast cleaning of randomly
sheared genomic or transcriptomic data.
- clone_filter - take a set of paired-end reads and reduce them according to PCR clones
(a PCR clone is a pair of reads that match exactly, while paried-end reads from two different DNA molecules will nearly
always be slightly different lengths).
- kmer_filter - allows paired or single-end reads to be filtered according to the number or
rare or abundant kmers they contain. Useful for both RAD datasets as well as randomly sheared genomic or transcriptomic data.
- denovo_map.pl - executes each of the stacks components to create a genetic linkage map, or
to identify the alleles in a free-standing population. It also handles uploading data to the database.
- ref_map.pl - takes reference-aligned input data and executes each of the stacks components,
using the reference alignment to form stacks, and identifies alleles. Can be used in a genetic map of a free-standing
population. It also handles uploading data to the database.
- load_radtags.pl - takes a set of data produced by either the denovo_map.pl
or ref_map.pl progams (or produced by hand) and loads it into the database. This allows the data
to be generated on one computer, but loaded from another. Or, for a database to be regenerated without re-executing the pipeline.
- index_radtags.pl - indexes the database to speed execution in the web interface
after all of the data has been loaded.
- export_sql.pl - provides for the export of all of the Stacks data in a compact form. For
each locus, the script reports the consensus sequence, the number of parents and progeny that Stacks could find the locus
in, the number of SNPs found at that locus and a listing of the individual SNPs and the observed alleles, followed by
the particular allele observed in each individual. The script allows you to specify a number of filters to the data.
- sort_read_pairs.pl - collates paired-end sequences for each catalog locus.
- exec_velvet.pl - executes Velvet on the collated set of reads for each catalog locus.