Stacks

exec_velvet.pl

This program executes Velvet on the collated set of reads for each catalog locus. It will then extract out the assembled contigs and write them to a file called collated.fa.

Program Options

exec_velvet.pl -p path -s path [-l path] -o path [-c] [-H len] [-P] [-I len] [-C exp_cov] [-T cov_cut] [-W file_white_list] [-w marker_white_list] [-L] [-e path] [-d] [-h]

Example Usage

~/% exec_velvet.pl -s ./pairs/ -o ./assembled/ -c -e /usr/local/bin -M 200

Other Pipeline Programs

Raw Reads

Core

Execution control

Utilities