Genome (Phred Phrap Consed)

Category(ies): Bioinformatics

Version:
phred version: 0.020425.c, phrap version 0.990329, phd2fasta version: 0.990622.f, phredPhrap 030415, Version 15.0 (050831)

Author / Distributor: Laboratory of Phil Green, University of Washington

Description:

Phrap/Phred/Consed are the data analysis tools

Phrap - Program for shotgun sequence assembly
Phred - Base calling software with quality estimation
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.
Cross_match - a general-purpose utility for comparing any two sets of (long or short) DNA sequences.

altix: running program | Documentation | Installation | System

Running Program:

mkdir chromat_dir edit_dir phd_dir
...
cd edit_dir
phredPhrap

the chromat files in "chromat_dir" as input file.

Documentation: http://www.phrap.org/phredphrapconsed.html

Installation:

Source code downloaded from http://www.phrap.org/consed/consed.html#howToGet
Compiled by gcc

System(s): Unix

inQuiry: not available at inQuiry

pcluster: Not available on pcluster

rcluster,IOB: running program | Documentation | Installation | System

Running Program: also refer to submit jobs to queues at rcluster,IOB

To run applications manually, e.x.
the chromat files in "chromat_dir" as input file.

mkdir chromat_dir edit_dir phd_dir
...
cd edit_dir
bsub -q queueName phrap C05D11.reads.screen -minmatch 20 -new_ace > phrap.out

To run interactive phredPhrap, conced, use inter1 node, also refer to running interactive jobs at rcluster, IOB

[username@rcluster ~]$ ssh inter1
[username@inter1 ~]$ mkdir chromat_dir edit_dir phd_dir
...
[username@inter1 ~]$ cd edit_dir
[username@inter1 ~]$ phredPhrap

For Mac user, make sure X11 available, then use following commands:

[username@rcluster ~]$ ssh -X inter1
[username@inter1 ~]$ mkdir chromat_dir edit_dir phd_dir
...
[username@inter1 ~]$ cd edit_dir
[username@inter1 ~]$ phredPhrap

To exit interactive node

[username@inter1 ~]$ exit
[username@rcluster ~]

Documentation: Same as altix

Installation: Same as altix

System(s): Unix