Stacks
Stacks is a software pipeline for building loci from short-read sequencing data, especially restriction enzyme-based approaches such as RAD-seq and GBS. It is commonly used for genetic mapping, population genomics, and phylogeography.
To load Stacks on Palmetto 2:
module load biocontainers
module load stacks
Stacks is modular and includes tools for read processing, catalog creation, genotyping, and population-level analysis. Common components include:
| Component | Purpose |
|---|---|
| process_radtags | Demultiplex and quality-filter RAD/GBS reads |
| ustacks/cstacks | Build loci per sample and create a catalog across samples |
| sstacks | Match sample loci against the catalog |
| gstacks | Assemble loci and call SNPs/alleles |
| populations | Compute population statistics and export results (e.g., VCF, STRUCTURE, PHYLIP) |
| denovo_map.pl/ref_map.pl | Run end-to-end de novo or reference-based workflows |
An example command workflow might look like:
process_radtags -p raw_reads/ -o cleaned_reads/ -b barcodes.txt -e pstI -r -c -q
ustacks -f cleaned_reads/sample_01.fq.gz -o stacks/ -i 1 -M 4 -p 8
cstacks -P stacks/ -M population_map.tsv -n 2 -p 8
sstacks -P stacks/ -M population_map.tsv -p 8
gstacks -P stacks/ -M population_map.tsv -t 8
populations -P stacks/ -M population_map.tsv --vcf -t 8
For usage details, examples, and parameter guidance, please see the Stacks documentation.
Parallel Capabilities: Multithreading is available for several components; see each command's documentation.