May 26, 2018
Phrap is a program for assembling shotgun DNA sequence data
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.