Stacks: ustacks

Program Options

ustacks -f in_path -o out_path [-M max_dist] [-m min_readds] [-t num_threads]

-f,--file — input file path.
-o,--out-path — output path to write results.
-M — Maximum distance (in nucleotides) allowed between stacks (default 2).
-m — Minimum number of reads to seed a stack (default 3).
-N — Maximum distance allowed to align secondary reads to primary stacks (default: M + 2).
-t,--threads — enable parallel execution with num_threads threads.
-i,--in-type — input file type. Supported types: fasta, fastq, gzfasta, or gzfastq (default: guess).
-n,--name — a name for the sample (default: input file name minus the suffix).
-R — retain unused reads.
-H — disable calling haplotypes from secondary reads.

--force-diff-len — allow raw input reads of different lengths, e.g. after trimming (default: ustacks perfers raw input reads of uniform length).
--keep-high-cov — disable the algorithm that removes highly-repetitive stacks and nearby errors.
--high-cov-thres — highly-repetitive stacks threshold, in standard deviation units (default: 3.0).
--max-locus-stacks — maximum number of stacks at a single de novo locus (default 3).
--k-len [len] — specify k-mer size for matching between alleles and loci (automatically calculated by default).
--deleverage — enable the Deleveraging algorithm, used for resolving over merged tags.

--max-gaps — number of gaps allowed between stacks before merging (default: 2).
--min-aln-len — minimum length of aligned sequence in a gapped alignment (default: 0.80).
--disable-gapped — do not preform gapped alignments between stacks (default: gapped alignements enabled).

--alpha [num] — chi square significance level required to call a heterozygote or homozygote, either 0.1, 0.05 (default), 0.01, or 0.001.

--bound-low [num] — lower bound for epsilon, the error rate, between 0 and 1.0 (default 0).
--bound-high [num] — upper bound for epsilon, the error rate, between 0 and 1.0 (default 1).

Here we run ustacks independently on four samples from a genetic cross, two parents and two progeny. We specify the parameters for creating putative alleles (-m) and merging alleles into putative loci (-M). We speed up the matching process by specifying 16 parallel threads.
% ustacks -f ./samples/f0_male.fq.gz -o ./stacks -m 3 -M 4 -t 16 % ustacks -f ./samples/f0_female.fq.gz -o ./stacks -m 3 -M 4 -t 16 % ustacks -f ./samples/progeny_01.fq.gz -o ./stacks -m 3 -M 4 -t 16 % ustacks -f ./samples/progeny_02.fq.gz -o ./stacks -m 3 -M 4 -t 16
Here we run ustacks against three samples from a population. Gapped alignments will be made between alleles when forming putative loci, by default.
% ustacks -f ./samples/sample_39-1.fq.gz -o ./stacks -M 6 -t 8 % ustacks -f ./samples/sample_40-2.fq.gz -o ./stacks -M 6 -t 8 % ustacks -f ./samples/sample_41-1.fq.gz -o ./stacks -M 6 -t 8