Gap5

Gap5

Gap5

Overview

Gap5 is a DNA sequence assembly visualiser and editing tool. It permits low level base by base editing as well as larger scale contig rearrangements such as complementing, joining and breaking apart contigs.

Input and outputs supported include SAM, BAM and CRAM file formats along with the less used formats CAF and ACE.

Gap5 is part of the Staden Package, a broad set of software tools originally developed for many years by Rodger Staden at the MRC Laboratory of Molecular Biology, Cambridge UK.

Download and Installation

Go to the https://sourceforge.net/projects/staden/ project page and follow the links to files -> staden. (https://sourceforge.net/projects/staden/files/staden/). Gap5 is one of the tools included in the Staden Package.

License and Citation

BSD Open Source License.

Contact

James Bonfield <jkb@sanger.ac.uk>

Authors

Sanger Contributors

Publications