Genome Assembly and Annotation Team

The assembly and annotation team carries out genome projects — sequencing, assembling and annotating genomes de novo. Because we specialize in large eukaryotic genomes and transcriptomes, genome sequence assembly is challenging, not only because of the sheer size of the data and computational requirements, but also due to repetitive elements, polyploidy and variation (single-nucleotide, insertions/deletions, and larger structural variants). We aim to meet these challenges by developing new computational protocols as each project demands. In particular, we are focusing our efforts on the adoption of nanopore-based single molecule long-read technology for both genomic DNA and messenger RNA sequencing. This year we have successfully applied hybrid assembly methods to the sequencing of a number of species including birds, amphibians, fish, insects, plants, fungi. Our rapid and robust annotation pipeline, which we are constantly improving, helps us understand these genomes by automatically integrating statistical models of coding DNA with evidence such as transcribed sequences and protein homology.

• Genome sequence assembly
• Gene prediction/genome annotation
• Transcriptome reconstruction
• Functional annotation