phred
Software Description
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.
Info
Module Name
phred
Last Updated On
08/29/2023
Support Level
Secondary Support
Software Access Level
Open Access
Home Page
Documentation
Software Description
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.
General Linux
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.
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