James Bonfield

Principal Software Developer

James is an author of computer software used by "finishers" - people manually editing and correcting sequence assemblies - and is also the primary developer of the C implementation of the CRAM file format. He also helps to maintain the widely used Samtools and Htslib packages.

I am the primary author and maintainer of Gap5 a sequence assembly visualiser and editor permitting high level contig editing (joining, breaking) along with low level base by base editing if desired.

I have a keen research interest in data compression techniques, some are which are found in htscodecs and fqzcomp5. Some of this work has made its way into the CRAM file format, of which I co-maintain the specification and am the author of the C implementation. This work is incorporated into the htslib/samtools packages.

My timeline

• Runner-up in Global Data Compression Competition task 2.

• Winner of SequenceSqueeze competition

• Started work at: Wellcome Trust Sanger Institute: Cambridge, United Kingdom

• Started work at: Laboratory of Molecular Biology: Cambridge, United Kingdom

• BSc Computer Science, University of Warwick