Publications by authors named "James Bonfield"

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CRAM 3.1: advances in the CRAM file format.
James K Bonfield

Bioinformatics· March 2022

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GA4GH: International policies and standards for data sharing across genomic research and healthcare.
Heidi L Rehm, Angela J H Page, Lindsay Smith, Jeremy B Adams, Gil Alterovitz, James K Bonfield

Cell Genom· November 2021

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Twelve years of SAMtools and BCFtools.
Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan

Gigascience· February 2021

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HTSlib: C library for reading/writing high-throughput sequencing data.
James K Bonfield, John Marshall, Petr Danecek, Heng Li, Valeriu Ohan

Gigascience· February 2021

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Crumble: reference free lossy compression of sequence quality values.
James K Bonfield, Shane A McCarthy, Richard Durbin

Bioinformatics· January 2019

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De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms.
Francesca Giordano, Louise Aigrain, Michael A Quail, Paul Coupland, James K Bonfield

Sci Rep· June 2017

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Comparison of high-throughput sequencing data compression tools.
Ibrahim Numanagić, James K Bonfield, Faraz Hach, Jan Voges, Jörn Ostermann

Nat Methods· December 2016

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The Scramble conversion tool.
James K Bonfield

Bioinformatics· October 2014

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Compression of FASTQ and SAM format sequencing data.
James K Bonfield, Matthew V Mahoney

PLoS One· September 2013

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Gap5--editing the billion fragment sequence assembly.
James K Bonfield, Andrew Whitwham

Bioinformatics· July 2010

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Genome-wide end-sequenced BAC resources for the NOD/MrkTac() and NOD/ShiLtJ() mouse genomes.
Charles A Steward, Sean Humphray, Bob Plumb, Matthew C Jones, Michael A Quail, James Bonfield

Genomics· February 2010

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Improvements to services at the European Nucleotide Archive.
Rasko Leinonen, Ruth Akhtar, Ewan Birney, James Bonfield, Lawrence Bower

Nucleic Acids Res· January 2010

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Petabyte-scale innovations at the European Nucleotide Archive.
Guy Cochrane, Ruth Akhtar, James Bonfield, Lawrence Bower, Fehmi Demiralp

Nucleic Acids Res· January 2009

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Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database.
Guy Cochrane, Ruth Akhtar, Philippe Aldebert, Nicola Althorpe, Alastair Baldwin, James Bonfield

Nucleic Acids Res· January 2008

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A genome-wide, end-sequenced 129Sv BAC library resource for targeting vector construction.
David J Adams, Michael A Quail, Tony Cox, Louise van der Weyden, Barbara D Gorick, James K Bonfield

Genomics· December 2005

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Shotgun haplotyping: a novel method for surveying allelic sequence variation.
Sarah J Lindsay, James K Bonfield, Matthew E Hurles

Nucleic Acids Res· October 2005

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Complex haplotypes, copy number polymorphisms and coding variation in two recently divergent mouse strains.
David J Adams, Emmanouil T Dermitzakis, Tony Cox, James Smith, Rob Davies, James Bonfield

Nat Genet· May 2005

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Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags.
Simon J Hubbard, Darren V Grafham, Kevin J Beattie, Ian M Overton, Stuart R McLaren, James K Bonfield

Genome Res· January 2005

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ZTR: a new format for DNA sequence trace data.
James K Bonfield, Rodger Staden

Bioinformatics· January 2002

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Trev: a DNA trace editor and viewer.
James K Bonfield, Kathryn F Beal, Matthew J Betts, Rodger Staden

Bioinformatics· January 2002

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