Minnesota Supercomputing Institute
Wednesday, December 7, 2016
Phred - Base calling software with quality estimation; Phrap - Program for shotgun sequence assembly; Consed - Sequence assembly editor companion to Phrap; Swat and CrossMatch - Sequence alignment tools; Phrapview - A graphical tool that provides a "global" view of the phrap assembly, complementary to the "local" view provided by the Consed.
To load this software in a Linux environment run the command:
module load phred phrap consed
Create two directories named chromat_dir and phd_dir and copy your sequence chromatogram files into chromat_dir. Create vector.seq file with your vector DNA sequence data in fasta format. Then you can execute these programs directly from the command line. eg
phred -id chromat_dir -pd phd_dir
phd2fasta -id phd_dir -os seqs_fasta -oq seqs_fasta.screen.qual
cross_match seqs_fasta vector.seq -minmatch 12 -minscore 20 -screen > screen.out
phrap seqs_fasta.screen -new_ace > phrap.out
Or, use these scripts like phredPhrap directly at edit_dir subdirectory.
Documentation is available for the following:
Phred --the base-caller
Phrap -- the assembler
Consed and Autofinish -- A Graphical Editor and Automated Finishing Program for Phrap Sequence Assemblies
general documentation on swat, crossmatch, phrap, and phrapview