phrap program to perform shotgun assembly. Output
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.
Phrap is not included as part of the Staden Package. It is available from
Phil Green.
Green, P. http://www.genome.washington.edu/UWGC/analysistools/phrap.htm.