Phrap is a program for assembling shotgun DNA sequence data. It allows use of entire sequence reads (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 is required and/or recommended by some packages available on Bio-Linux such as gap4 (Staden), stars, and partigene. Please also see the documentation on gcphrap if you use the Staden package.

Phrap is licensed software and thus is not installed by default on Bio-Linux. It is free to academic researchers but you must obtain a license. Further information on how to obtain phrap is available on the official website for phred, phrap and consed.

If and only if you have already obtained a license to use phred or phrap (cross_match is found within the phrap package), the NEBC can provide you with packages that will install these programs onto Bio-Linux, including the staden-specific phrap extra: gcphrap. Please contact the NEBC helpdesk if you have your license and are ready to proceed.