Cap3 Assembly

Cap3 is not included as part of the Staden Package. It is available from Xiaoqiu Huang ( huang@mtu.edu ).

Description

This module uses the cap3 program to perform shotgun assembly. Output will be placed in the fofn.assembly directory, where fofn is the filename prefix listed in the "Files to Process" panel. The output is in a format suitable for directed assembly within gap4. This can also be performed by using the "Enter Assembly into Gap4" module. Cap3 differs from Cap2 in that it can make use of confidence values (in the range supplied from phred) and constraints.

Option: Auto-generate constraints

When enabled, this uses the reading direction (forward / reverse primers), the template name and the insert size, to produce a file containing data to constrain how the readings may be assembled.