The Genome Assembly and Annotation Team carries out “genome projects” in the classical sense, from design of the de novo sequencing strategy, on through assembly and annotation of the genome.
The team specializes in large eukaryotic genomes and transcriptomes, especially those of animals and plants. Other types of genomes analyzed include those of organelles, endosymbionts, metagenomes and metatranscriptomes, and cancer genomes. Genome assembly is not only difficult due to the sheer size of the data and computational requirements, but also because the biology of genomes is confounded by repetitive elements, polyploidy and variation (single-nucleotide, insertions/deletions, and larger structural variants). The team focuses its efforts on meeting and overcoming these challenges, incorporating new technologies and developing new computational protocols as each project demands.
Annotation of the gene content of the newly assembled genome is key to understanding the genome, once finished. On this front the teams has made progress in developing a rapid robust annotation pipeline, significantly cutting down the time required to annotate a genome.