Genome Reference Informatics Team | Human Genetics

Genome Reference Informatics Team | Human Genetics

Genome Reference Informatics Team

Genome Refernce InfomaticsSanger Institute, Genome Research Limited
Genome Refernce Infomatics

Our Research and Approach

The Genome Reference Informatics Team analyses genome assemblies to reveal and correct quality issues and to identify and add variation. The team consists of Senior Bioinformaticians and Senior Computer Biologists to cover software development, data analysis and genome curation. Besides comissioning sequencing and generation of other genome data (e.g. optical mapping), we develop bespoke software like gEVAL to identify and visualize genome assembly issues. This is used by our curators to resolve those issues through changes or additions to the assemblies. We are also creating de novo assemblies for individuals/strains.

Our team represents the Sanger Institute within the Genome Reference Consortium, and we work closely with our consortium partners and other collaborators to ensure access to the latest data and analyses. Assembly improvements are submitted to INSDC on a regular schedule.

People

Howe, Kerstin
Dr Kerstin Howe
Group Leader

Kerstin is a computational biologist whose primary interest is in the provision of accurate reference genome sequences and structures to support biological, agricultural and clinical science.

Key Projects, Collaborations, Tools & Data

The Genome Reference Informatics Team is responsible for the reference genome assemblies of human, mouse and zebrafish. We are also involved in the analysis and improvement of assemblies of 16 mouse strains, chicken, individual humans and additional zebrafish strains.

Partners and Funders

Internal Partners
External Partners and Funders

Publications

  • Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.

    Schneider VA, Graves-Lindsay T, Howe K, Bouk N, Chen HC et al.

    Genome research 2017;27;5;849-864

  • gEVAL - a web-based browser for evaluating genome assemblies.

    Chow W, Brugger K, Caccamo M, Sealy I, Torrance J and Howe K

    Bioinformatics (Oxford, England) 2016;32;16;2508-10

  • Using optical mapping data for the improvement of vertebrate genome assemblies.

    Howe K and Wood JM

    GigaScience 2015;4;10

  • The zebrafish reference genome sequence and its relationship to the human genome.

    Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C et al.

    Nature 2013;496;7446;498-503

  • Modernizing reference genome assemblies.

    Church DM, Schneider VA, Graves T, Auger K, Cunningham F et al.

    PLoS biology 2011;9;7;e1001091