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Stacks: assemble read pairs by locus (version 1.46.1)

Output from previous Stacks pipeline steps (e.g. denovo_map or refmap):

Files containing reads to assemble:

only R2 reads

White list of catalog IDs to include:

Minimum number of reads by locus:

Perform assembly with Velvet:

If not selected, the tool will only produce of collection of fasta files (one per locus) containing reads ready to assemble.

What it does

This program will run each of the Stacks sort_read_pairs.pl and exec_velvet.pl utilities to assemble pair-end reads from STACKS pipeline results

Input file

Output from denovo_map or ref_map

Output file

A collated.fa file containing assembled contigs for each locus

Created by:

Stacks was developed by Julian Catchen with contributions from Angel Amores, Paul Hohenlohe, and Bill Cresko

Project links:

Stacks website