What it does
phrap ("phragment assembly program", or "phil's revised assembly program"; a homonym of "frappe" = French for "swat") -- a program for assembling shotgun DNA sequence data. Key features: allows use of entire read (not just trimmed high quality part); uses a combination of user-supplied and internally computed data quality information to improve accuracy of assembly in the presence of repeats; constructs contig sequence as a mosaic of the highest quality parts of reads (rather than a consensus); provides extensive information about assembly (including quality values for contig sequence) to assist trouble-shooting; able to handle very large datasets.
phrap is great for assembling Sanger shotgun reads but should not be used for next-generation data (e.g. Illumina, Solid, 454, etc.). However phrap is useful for combining short-read assemblies from Velvet or Abyss (i.e. results from using multiple k-mer parameters). When used for this purpose, you should filter out short sequences first (e.g. less than 200-1000bp, depending on number of contigs).