cap3-contig-assembly-program

Genetics

Software Description

1

Info

Module Name

cap3

Last Updated On

08/29/2023

Support Level

Secondary Support

Software Access Level

Open Access

Home Page

http://seq.cs.iastate.edu/cap3.html

Documentation

Software Description

The contig assembly program (CAP) is an effective program for assembling DNA fragments. The CAP3 program includes a number of improvements and new features. The program has a capability to clip 5\' and 3\' low-quality regions of reads. It uses base quality values in computation of overlaps between reads, construction of multiple sequence alignments of reads, and generation of consensus sequences. The program also uses forward-reverse constraints to correct assembly errors and link contigs. Results of CAP3 on four BAC data sets are presented. The performance of CAP3 was compared with that of PHRAP on a number of BAC data sets. PHRAP often produces longer contigs than CAP3 whereas CAP3 often produces fewer errors in consensus sequences than PHRAP. It is easier to construct scaffolds with CAP3 than with PHRAP on low-pass data with forward-reverse constraints.

General Linux

To load this module for use in a Linux environment, you can run the command:

module load cap3

Depending on where you are working, there may be more than one version of cap3 available. To see which modules are available for loading you can run:

module avail cap3

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