Table 1  Stacks component programs
ProgramDescriptionInputsDatabase interaction
process_radtags.plCleans raw Illumina reads, outputs FASTA/FASTQ files.Raw Illumina readsNo
ustacks (unique stacks)Builds loci de novo and detects haplotypes in one individual.Cleaned FASTA/FASTQ filesNo
cstacks (catalog stacks)Merges loci from multiple individuals to form a catalog.ustacks, tab-separated filesNo
sstacks (search stacks)Matches loci from an individual against a catalog.ustacks and cstacks, tab-separated filesNo
markers.plCalls mappable markers from parental loci.NoneYes
index_radtags.plIndexes the database for use by the web interface.NoneYes
denovo_map.plExecutes ustacks on each individual, builds a catalog with cstacks, and matches individuals against the catalog with sstacks. Calls markers with markers.pl and indexes the database with index_radtags.pl.Cleaned FASTA/FASTQ filesYes
genotypes.plCalls genotypes in a map cross population and outputs markers for use by JoinMap or r/QTL.NoneYes
pstacks (population stacks)Takes cleaned reads aligned to a reference genome, builds stacks based on the genomic locations of the reads, and detects haplotypes in one individual.Bowtie or SAM sequence alignmentsNo
ref_map.plExecutes pstacks on each individual, builds a catalog with cstacks, and matches individuals against the catalog with sstacks. Calls markers with markers.pl and indexes the database with index_radtags.pl.Cleaned FASTA/FASTQ filesYes
sort_read_pairs.plGiven a set of Stacks data and a set of cleaned, paired-end Illumina reads, outputs one FASTA file for each stack consisting of the paired-end reads associated with reads in that stack.ustacks output files, cleaned FASTA/FASTQ filesNo
load_sequences.plLoads a set of loci-associated sequences (e.g., RNA-seq ESTs) into the database.FASTA file containing sequencesYes
export_catalog.plExports sequences from the database, including loci and loci-related sequences.NoneYes