CONSED, PHRED and PHRAP: UNIX based Sequencer output to Contig Assembly
PHRED reads sequencer output files and "calls" the bases producing a text file with the sequence. PHRAP reads the PHRED sequences and assembles the sequences into a contig. A script file called phredPhrap runs both programs in the appropriate order. CONSED is a GUI program which uses PHRED/PRAP output to create consensus sequences,provide for display of the sequencer traces and allow for editing. CONSED, PHRED and PHRAP are available on the BCR UNIX workstations. Typing "phred" or "phrap" will launch the programs. Various scripts (PERL) may be used for controlling these two powerful programs. Various process associated programs such as phd2fasta (converts phred reads to fasta format) and cross_match (for stripping vector sequences) are now in the path and available for use as well. If you wish to use the CONSED program you MUST run PHRED and PHRAP by means of the phredPhrap script (see below). The phredPhrap script is a convenient and easy way to run PHRED and PHRAP. A companion program called POLYPHRED will scan sequences for polymorphisms. CONSED is a powerful controlling program which can display sequence project data, design primers, strip vectors, display sequencing traces and calculate consensus sequences. In order to use CONSED you must be either sitting at an SGI workstation OR running and x-server software (eg Hummingbird Exceed) on your PC or MAC (OSX.3 or later with X11 installed). The CONSED/PHRED/PHRAP programs expect datafiles to be in particular places. There are a couple of compressed sample datafiles below which will set up a proper directory structure and populate the directories. For use with your own data, you are obliged to set up a "typical" directory structure which resembles the example directories. For instance these four subdirectories chromat_dir chromats_to_add edit_dir phd_dir As is often the case with BCR programs you will need to set an environment variable for PHRED to operate properly here at MUSC. You will need to type the following lines: setenv PHRED_PARAMETER_FILE /usr/common/bcr/genome/lib/phredpar.dat setenv CONSED_HOME /usr/common/bcr/genome set path=($path $CONSED_HOME/bin) The above lines should also be placed into your ".cshrc" file if you anticipate that you will use the program regularly. PHRED was designed to read sequencer output data including chromatograms. Note in the manual the details regarding location of the input sequence and chromatogram files. PHRAP was designed to perform shotgun sequence assembly based on input from the PHRED program. CONSED was designed to read PHRAP/PHRED output files and perform some sophisticated analyses. The manual shows you the ropes for using CONSED. POLYPHRED was designed to examine data for polymorphisms and integrates nicely with the CONSED/PHRED/PHRAP programs. Here are a some links to test data files for you to experiment with in using CONSED, phredPhrap and polyphred standard.tar.gz. polyphred.tar.gz example.tar.gz csft2.tar.gz Download the file onto your HOMEROOM directory. Type: gunzip standard.tar.gz tar -xvf standard.tar gunzip polyphred.tar.gz tar -xvf polyphred.tar These will create a directory called standard and another called polyphred. Within each directory are four subdirectories filled with test data. cd to the respective edit_dir and there type "phredPhrap" for the standard data. When it completes, type "consed_sgi &" from the same directory to launch the CONSED program and allow you to view the sequences and the traces and evaluate the contigs. The polyphred dataset has been pre-analyzed by the polyphred program and can be launched directly with consed from the polyphred/edit_dir directory. The example and csft2 data need to be first digested by phredPhrap then polyphred and finally are ready for consed.
The BCR at the Medical University of South Carolina
URL: http://bcr.musc.edu/
e-mail to Starr comments about this page.