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Computational Genomics


The Computational Genomics team, led by Sarah Ayling, is responsible for implementing and executing high-throughput analysis pipelines to analyse plant, animal and viral genomes. Team interests include:

  • Exploring assembly strategies for next generation data
  • The impact of genome characteristics such as repeat content and ploidy
  • Variant calling (genome association studies)
  • Virus transmission studies

The Crop Genomics team has a focus on analysing plant species of agricultural interest; current species of interest include: wheat, barley and rice.


The Computational Genomics team is also part of the BBSRC funded LoLa project “Wheat Genomics for Sustainable Agriculture” . The project aims to generate wheat gene models assigned to specific chromosome arms, and improved assemblies for wheat chromosomes 2B, 4B and 4D.

As part of the UK's barley sequencing consortium, they have been analysing barley RNA-Seq data in collaboration with the James Hutton Institute. In addition, they will be calling variants from exome capture data from diverse barley lines.

The team is part of the EU TransPLANT project “Trans-national infrastructure for plant genomic science”, where they lead the work package on implementation of resource-intensive algorithms for plant genomics data. The team's focus is on the evaluation and development of strategies for genome sequencing and assembly.

In addition they are working on several virus projects with collaborators from the Centre for Virus Research, Institute for Animal Health and the Animal Health Trust.

As part of the International Wheat Genome Sequencing Consortium , the Crop Genomics team is working to assemble flow-sorted chromosome arms for the Chromosome Survey Sequence of hexaploid bread wheat. Assembled chromosomes are available from URGI .

Future Developments

The team are working to develop and implement methods for reference-free quality assessment of sequence assemblies. In addition they will continue to explore different assembly strategies for genomes and transcriptomes, including hybrid-assemblies, next generation sequencing of BACs and integration of optical-mapping data.

Selected Publications
  • Groenen M.A.M, et al. Pig genomes provide insight into porcine demography and evolution (accepted)
  • The International Barley Genome Sequencing Consortium (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature doi:10.1038/nature11543
  • D. Earl et al. Assemblathon 1: A competitive assessment of de novo short read assembly methods. Genome Research, 21(12):2224–2241, December 2011. See
  • Clavijo B., Ayling S., Caccamo M. “Quality metrics for assessing de novo assemblies” ECCB 2012, September 2012, Basel, Switzerland
  • Leggett R., Ramirez-Gonzalez R., Caccamo M., “MetaCortex: Classification of short read sequences from environmental samples” Genome Informatics, September 2012, Cambridge, UK
  • Enriquez-Gasca M.R., Ayling S., Murcia P., Caccamo M. "Intra-and inter-host evolutionary dynamics of mammalian influenza viruses”  17th international bioinformatics workshop on Virus Evolution and Molecular Epidemiology, September 2012, Serbia
  • Sampath D., Ayling S., Swarbreck D., Febrer M., Hedley P.E., Pfeifer M., Steuernagel B., Mayer K., Waugh R., Caccamo M., Rogers J. “A comparison of approaches for RNA-Seq differential expression analysis in barley” –  UK-NGS Meeting  August 2012, Nottingham, UK
  • Clark M., Leggett R., Heavens D., Vasoya D., Drou N., CaccamoM. “The long and the short of it: de novo assembly of extreme GC content microbial genomes”, The Biology of Genomes, Cold Spring Harbor, May 2012.
  • Ramirez-Gonzalez R., Leggett R., Caccamo M. “Efficient short-read assemblies with paired-end k-mers”, Genome Informatics, Cold Spring Harbor, November 2011.
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