# phred

## Summary

+ **Module Name:** phred
+ **Support Level:** Secondary Support
+ **Software Access Level:** Open Access
+ **Home Page:** [http://www.phrap.org/phredphrapconsed.html](http://www.phrap.org/phredphrapconsed.html)

## 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.