Stacks

sort_read_pairs.pl

This program will collate the paired-end sequences for each catalog locus. The sort_read_pairs.pl program will load the *.tags.tsv files (ustacks output) for each sample to know which reads were assembled into which stacks, the *.matches.tsv files (sstacks output) for each sample to know which stacks were matched to the same catalog locus, and the paired-end reads, which it will bin according to which catalog locus they belong.

Program Options

sort_read_pairs.pl -p path -s path -o path [-r reads] [-W white_list] [-w white_list] [-d] [-h]

Example Usage

% sort_read_pairs.pl -p ./stacks/ -s ./samples/ -o ./pairs/ -r 10 -w whitelist.tsv

Other Pipeline Programs

Raw Reads

Core

Execution control

Utilities