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.

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