CAP3

Description

cap3 website

This module enables the use of the CAP3 software We have made the following improvements to the CAP sequence assembly program. 1. Use of forward-reverse constraints to correct assembly errors and link contigs. 2. Use of base quality values in alignment of sequence reads. 3. Automatic clipping of 5' and 3' poor regions of reads. 4. Generation of assembly results in ace file format for Consed. 5. CAP3 can be used in GAP4 of the Staden package. If you use CAP3 in any published work, please cite the following reference: Huang, X. and Madan, A. (1999) CAP3: A DNA sequence assembly program. Genome Res., 9, 868-877. The cap3 programs are available in this package are cap3, cap3-opteron, formcon, and formcon-opteron. All programs from the pcap distribution are also available via this module. See documentation at http://deepc2.psi.iastate.edu/aat/cap/capdoc.html

Environment Modules

Run module spider cap3 to find out what environment modules are available for this application.

Environment Variables

• HPC_CAP3_DIR - CAP3 directory
• HPC_CAP3_BIN - CAP3 executables directory
• HPC_CAP3_DOC - CAP3 docs directory
• HPC_CAP3_EXAMPLE - CAP3 examples directory

Categories

biology, assembly