Stacks

ustacks

The unique stacks program will take as input a set of short-read sequences and align them into exactly-matching stacks (or putative alleles). Comparing the stacks it will form a set of putative loci and detect SNPs at each locus using a maximum likelihood framework1.

1Hohenlohe PA, Bassham S, Etter PD, Stiffler N, Johnson EA, Cresko WA. 2010. Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genetics, 6(2):e1000862.

Program Options

ustacks -f file_path -i id -o path [-m min_cov] [-M max_dist] [-p num_threads] [-d] [-t file_type]

Stack assembly options:

Gapped assembly options:

Model options:

For the SNP or Bounded SNP model:

For the Bounded SNP model:

For the Fixed model:

Example Usage

Here we run ustacks against four samples from a genetic cross, two parents and two progeny. We assign each sample its own unique integer ID (-i) and we specify the parameters for creating putative alleles (-m) and mergin alleles into putative loci (-M). We speed up the matching process by specifying 15 parallel threads.

% ustacks -f ./samples/f0_male.fq -o ./stacks -i 1 -m 3 -M 4 -p 15 % ustacks -f ./samples/f0_female.fq -o ./stacks -i 2 -m 3 -M 4 -p 15 % ustacks -f ./samples/progeny_01.fq -o ./stacks -i 3 -m 3 -M 4 -p 15 % ustacks -f ./samples/progeny_02.fq -o ./stacks -i 4 -m 3 -M 4 -p 15

Here we run ustacks against three samples from a population and we are allowing gapped alignments between alleles when forming putative loci.

% ustacks -f ./samples/sample_39-1.fq.gz -o ./stacks -i 1 -M 6 --gapped -p 15 % ustacks -f ./samples/sample_40-2.fq.gz -o ./stacks -i 2 -M 6 --gapped -p 15 % ustacks -f ./samples/sample_41-1.fq.gz -o ./stacks -i 3 -M 6 --gapped -p 15

Other Pipeline Programs

Raw Reads

Core

Execution control

Utilities