Vital to Chromaseq's processing of chromatograms are the programs Phred and Phrap. Phred (Green and Ewing, 2002) is a program that examines chromatogram files, and makes base calls therefrom. It also judges the quality of the base calls, and assigns a score to each called base. Phrap ("Phil's Revised Assembly Program"; Green, 1999) is a program that takes the output of Phred, and forms contigs of the reads, producing in the process and ACE file. These programs were originally written for large-scale sequencing efforts such as the Human Genome Project. Their source code is currently (2005) available free for most academic uses; compiled versions are available for a cost. Additional details about these two programs, including how to obtain their source code, is available on the Phred and Phrap web site. See the Installation page in this manual for hints on acquiring, compiling and installing Phred & Phrap.
In the context of Chromaseq, you will need to specify the location of the programs that Chromaseq uses. Phred, Phrap, and Phd2Fasta must all be in the same directory, which you will specify in the first field of the Phred Phrap Locations and Options dialog box. You will also need to specify the location of the phredpar.dat file, as described on the Installation page.
You may optionally add some command-line arguments to be sent to Phred or Phrap in the script. For details of the command-line arguments that are available, see the documentation that comes with Phred and Phrap. (For standard use, you will not need to alter the default settings in Chromaseq.)
References
Green, P. 2009. Phrap, version 1.090518. http://phrap.org. [You should cite whatever version you are using.]
Green, P. and Ewing, B. 2007. Phred, version 0.071220.c. http://phrap.org. [You should cite whatever version you are using.]