Author

James Bonfield

Wellcome Sanger InstituteORCID 0000-0002-6447-4112Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Assay:whole-genome sequencing· 5 Approach:experimental assay· 2 Research Focus:benchmarking· 1 Research Focus:database / resource· 1 Research Focus:genome assembly· 1 Approach:optimal transport· 1 Research Focus:software / tool· 1 Approach:statistical model· 1

Frequent Co-Authors

Heng LiiD· 2 shared Richard Michael DurbiniD· 2 shared Andrew WhitwhamiD· 1 shared Bastien ChevreuxiD· 1 shared Chenxi ZhouiD· 1 shared John MarshalliD· 1 shared Josh CudbyiD· 1 shared Peter J. A. CockiD· 1 shared

Activity by Year

2015-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 16 mutual co-author links

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2 shared papersBioinformatics

Heng LiORCID

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Author profile →

5 papers

Recent·Most cited

Pangenome-guided sequence assembly via binary optimisation

Josh Cudby, James Bonfield, Chenxi Zhou, Richard Michael Durbin, Sergii Strelchuk

This paper introduces a pangenome-guided sequence assembly framework that reduces contigs in complex regions using graph traversal optimisation, with potential for quantum computing implementation.

bioRxiv · Aug 6, 2025 · PreprintGenomics

CRAM 3.1: Advances in the CRAM Format

James Bonfield

CRAM 3.1 improves compression efficiency for DNA sequencing data, reducing file sizes by 7-15% compared to CRAM 3.0 and 50-70% compared to BAM for Illumina data.

Bioinformatics · Jan 4, 2022Peer-reviewedBioinformatics

HTSlib - C library for reading/writing high-throughput sequencing data

James Bonfield, John Marshall, Petr Danecek, Heng Li, Valeriu Ohan, Andrew Whitwham, Thomas Keane, Robert M. Davies

HTSlib provides a C library for efficient programmatic access to high-throughput sequencing data formats, with performance improvements and new features.

GigaScience · Jan 29, 2021Peer-reviewedBioinformatics

Crumble: reference free lossy compression of sequence quality values

James Bonfield, Shane McCarthy, Richard Michael Durbin

Crumble compresses sequence quality values in CRAM files to reduce storage while preserving variant calling accuracy.

Bioinformatics · Jul 9, 2018Peer-reviewedBioinformatics

SAM/BAM format v1.5 extensions for de novo assemblies

Peter J. A. Cock, James Bonfield, Bastien Chevreux, Heng Li

The paper updates the SAM/BAM format to support de novo assemblies by adding features like padded references and embedded sequences.

bioRxiv · May 29, 2015 · PreprintBioinformatics