Phrap is a program for assembling shotgun DNA sequence data.
Among other features, it allows use of the entire read and not just the
trimmed high quality part, it uses a combination of user-supplied and
internally computed data quality information to improve assembly accuracy
in the presence of repeats, it constructs the contig sequence as a mosaic
of the highest quality read segments rather than a consensus, it provides
extensive assembly information to assist in trouble-shooting assembly
problems, and it handles large datasets.

This package also contains Swat and Cross_match.
Swat is a program for searching one or more DNA or protein query sequences
against a sequence database, using (an efficient implementation of) the
Smith-Waterman-Gotoh algorithm.
Cross_Match is a general-purpose utility based on Swat for comparing any
two sets of DNA sequences, and it can be used to:
* produce vector-masked versions of a set of reads
* compare a set of cDNA sequences to a set of cosmids
* compare contigs found by two altanative assembly procedures to each other
* compare phrap contigs to the final edited cosmid sequence.

WWW: http://www.phrap.org/phredphrapconsed.html