Phrap 

"Phragment assemble program"  or « Phil’s revised assembly program » 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.Phrap searches for reads with matching words and then does a SWAT comparisn between pairs, to identify possible overlaps. Then it masks vetor sequences, identifies near duplicate reads, construct contig layouts based on strong pairwise alignments and identify inconsistencies. Phrap returns Phred-like quality scores for each base of the contig.( http://www.phrap.org/phredphrapconsed.html, Edwards 2009)