James Bonfield | Principal Software Developer

Bonfield, James

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, used within Samtools/Htslib.

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 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 in the htslib/samtools packages.

Publications

  • Comparison of high-throughput sequencing data compression tools.

    Numanagić I, Bonfield JK, Hach F, Voges J, Ostermann J et al.

    Nature methods 2016;13;12;1005-1008

  • The Scramble conversion tool.

    Bonfield JK

    Bioinformatics (Oxford, England) 2014;30;19;2818-9

  • Compression of FASTQ and SAM format sequencing data.

    Bonfield JK and Mahoney MV

    PloS one 2013;8;3;e59190

  • Gap5--editing the billion fragment sequence assembly.

    Bonfield JK and Whitwham A

    Bioinformatics (Oxford, England) 2010;26;14;1699-703

  • Petabyte-scale innovations at the European Nucleotide Archive.

    Cochrane G, Akhtar R, Bonfield J, Bower L, Demiralp F et al.

    Nucleic acids research 2009;37;Database issue;D19-25

  • Comparison of high-throughput sequencing data compression tools.

    Numanagić I, Bonfield JK, Hach F, Voges J, Ostermann J et al.

    Nature methods 2016;13;12;1005-1008

  • Gap5--editing the billion fragment sequence assembly.

    Bonfield JK and Whitwham A

    Bioinformatics (Oxford, England) 2010;26;14;1699-703

  • Genome-wide end-sequenced BAC resources for the NOD/MrkTac() and NOD/ShiLtJ() mouse genomes.

    Steward CA, Humphray S, Plumb B, Jones MC, Quail MA et al.

    Genomics 2010;95;2;105-10

  • Improvements to services at the European Nucleotide Archive.

    Leinonen R, Akhtar R, Birney E, Bonfield J, Bower L et al.

    Nucleic acids research 2010;38;Database issue;D39-45

  • Petabyte-scale innovations at the European Nucleotide Archive.

    Cochrane G, Akhtar R, Bonfield J, Bower L, Demiralp F et al.

    Nucleic acids research 2009;37;Database issue;D19-25

  • Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database.

    Cochrane G, Akhtar R, Aldebert P, Althorpe N, Baldwin A et al.

    Nucleic acids research 2008;36;Database issue;D5-12

  • A genome-wide, end-sequenced 129Sv BAC library resource for targeting vector construction.

    Adams DJ, Quail MA, Cox T, van der Weyden L, Gorick BD et al.

    Genomics 2005;86;6;753-8

  • Shotgun haplotyping: a novel method for surveying allelic sequence variation.

    Lindsay SJ, Bonfield JK and Hurles ME

    Nucleic acids research 2005;33;18;e152

  • Complex haplotypes, copy number polymorphisms and coding variation in two recently divergent mouse strains.

    Adams DJ, Dermitzakis ET, Cox T, Smith J, Davies R et al.

    Nature genetics 2005;37;5;532-6

  • Automated detection of point mutations using fluorescent sequence trace subtraction.

    Bonfield JK, Rada C and Staden R

    Nucleic acids research 1998;26;14;3404-9

Career/Research Highlights

Bonfield, James
James's Timeline
2011

Winner of SequenceSqueeze competition

2003

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

1992

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

1989

BSc Computer Science, University of Warwick