Phrap is assembly software developed and distributed at the University of Washington, USA. It is most commonly used with its companion base-calling program, Phred. Phred takes trace files as input, re-calls the bases and assigns a quality score to each base call.
The quality score that Phred assigns is claimed to reflect the probability that the call is correct. Specifically, the quality score, Q, is defined as:
Q = -10 log(base10) P, where P is the probability that the call is an error.
This means, for example, that with a score of 20, there is a 1 in 100 chance of error; with a score of 30, there is a 1 in 1000 chance of error; and with a score of 40, there is a 1 in 10,000 chance of error, etc. These probabilities have been estimated by analysis of Phred base calls that have been compared to base calls known to be correct.
Phred writes the base calls, quality scores, and base call locations for each trace file to a file with the same name as the trace file plus an extension of .phd.x, where x is a number. Unless you explicitly request the creation of the .phd files upon execution of Phred, the files will not be available later for importing.
Phrap assembles the sequences, writing the assembly information to a file with an extension of .ace. The .ace file contains each sequence, its original filename, its trim information, offset into the contig, direction, and sequence gaps.