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.

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

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, we have been analysing barley RNA-Seq data in collaboration with the James Hutton Institute. In addition, we will be calling variants from exome capture data from diverse barley lines.

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

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

• Sarah Ayling - Group Leader
• Paul Bailey - Scientific Programmer
• Bernardo Clavijo - Bioinformatics Assembly Algorithms Development Project Leader
• Rocio Enriquez Gasca - Scientific Programmer
• Dharanya Sampath - Scientific Programmer
• Jon Wright - Scientific Programmer

We are working to develop and implement methods for reference-free quality assessment of sequence assemblies. In addition we 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.

• 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 http://genome.cshlp.org/content/early/2011/11/02/gr.126599.111

• Bernardo Clavijo, Sarah Ayling, Mario Caccamo “Quality metrics for assessing de novo assemblies” ECCB 2012, September 2012, Basel, Switzerland
• Richard M. Leggett, Ricardo H. Ramirez-Gonzalez, Mario Caccamo, “MetaCortex: Classification of short read sequences from environmental samples” Genome Informatics, September 2012, Cambridge, UK
• Enriquez-Gasca MR, 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
• Dharanya Sampath, Sarah Ayling, David Swarbreck, Melanie Febrer, Pete E. Hedley, Matthias Pfeifer, Burkhard Steuernagel, Klaus Mayer, Robbie Waugh, Mario Caccamo, Jane Rogers “A comparison of approaches for RNA-Seq differential expression analysis in barley” –  UK-NGS Meeting  August 2012, Nottingham, UK
• Matthew Clark, Richard Leggett, Darren Heavens, Deepali Vasoya, Nizar Drou and Mario Caccamo, “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.
• Ricardo Ramirez-Gonzalez, Richard Leggett, Mario Caccamo, “Efficient short-read assemblies with paired-end k-mers”, Genome Informatics, Cold Spring Harbor, November 2011.