Phrap Assembly

Phrap is not included as part of the Staden Package. It is available from Phil Green. http://www.genome.washington.edu/UWGC/analysistools/phrap.htm

Description

This module uses the phrap 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. Phrap can make use of the confidence value information written by the phred program to produce better assemblies. Phrap also uses the full length of the sequence and will ignore any quality clipping. It is still necessary to clip sequencing vector.

Option: Minimum exact match

Minimum length of matching word for SWAT comparison.

Option: Minimum SWAT score

Minimum SWAT score.

Option: Other phrap arguments

Any other phrap command line arguments.