Perform contig assembly using CAP3

CAP3 Plugin

This plugin performs contig assembly with the popular program CAP3.

Quick Start

Install the plugin by downloading the gplugin file and dragging it in to Geneious Prime or use the plugin manager in Geneious Prime (under Tools - Plugins in the menu).

Once installed, run the plugin by selecting the nucleotide sequences to be assembled and choosing Align/Assemble - De Novo Assemble from the toolbar then picking CAP3 under Assembler in the options.

Before running the plugin you will need to set CAP3 executable to point to your copy of CAP3. CAP3 must be downloaded from the official CAP3 Website. Commercial users require a license from the author.


1.0 (12 Oct 2012) – Download


Huang, X. and Madan, A. (1999) CAP3: A DNA sequence assembly program. Genome Res., 9, 868-877.


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