Gap5 is a DNA sequence assembly visualiser and editing tool.

Gap5 permits low level base by base editing as well as larger scale contig rearrangements such as complementing, joining and breaking apart contigs.

About Gap5

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.


Go to the project page and follow the links to files -> staden. (

Gap5 is one of the tools included in the Staden Package.

Further information

BSD Open Source License.


If you need help or have any queries, please contact us using the details below.

James Bonfield

Sanger Institute Contributors

Photo of James Bonfield

James Bonfield

Principal Software Developer

Photo of Andrew Whitwham

Andrew Whitwham

Senior Software Developer

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