Open Access Highly Accessed Software

A database and API for variation, dense genotyping and resequencing data

Daniel Rios, William M McLaren, Yuan Chen, Ewan Birney, Arne Stabenau, Paul Flicek and Fiona Cunningham*

Author affiliations

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

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Citation and License

BMC Bioinformatics 2010, 11:238  doi:10.1186/1471-2105-11-238

Published: 11 May 2010



Advances in sequencing and genotyping technologies are leading to the widespread availability of multi-species variation data, dense genotype data and large-scale resequencing projects. The 1000 Genomes Project and similar efforts in other species are challenging the methods previously used for storage and manipulation of such data necessitating the redesign of existing genome-wide bioinformatics resources.


Ensembl has created a database and software library to support data storage, analysis and access to the existing and emerging variation data from large mammalian and vertebrate genomes. These tools scale to thousands of individual genome sequences and are integrated into the Ensembl infrastructure for genome annotation and visualisation. The database and software system is easily expanded to integrate both public and non-public data sources in the context of an Ensembl software installation and is already being used outside of the Ensembl project in a number of database and application environments.


Ensembl's powerful, flexible and open source infrastructure for the management of variation, genotyping and resequencing data is freely available at webcite.