Progress on the I5K Pilot at the Baylor College of Medicine Human Genome Sequencing Center

The i5K is an initiative to sequence the genomes of 5,000 arthropods of medical, agricultural and scientific importance. As a pilot project to identify potential challenges in species selection, identification and acquisition, DNA isolation, sequencing strategies, assembly, automated and manual annotation, analysis and publication, the BCM-HGSC is sequencing ~30 arthropods, selected by the i5K species selection committee.

We present our progress, working with 30 groups of collaborators including lessons from our attempts to obtain DNA, sequence and assemble multiple genomes in a production environment. Our automated annotation pipeline for arthropods provided high quality gene models and can scale to annotate 1,000’s of insect genomes. The annotation pipeline is based on the Maker pipeline, but uses extensive metazoan protein alignment evidence, RNAseq evidence from the species being sequenced, and automatic training of the ab-initio Augustus and SNAP gene predictors.

Additionally, approximately 30 evidence tracks are generated for the web-Apollo tool, enabling manual annotators to see all input evidence into a gene model. The 28 annotated species’ genomes are being hosted by the National Agricultural Library providing access via searching, community manual annotation support and browser functionality. We aim to port this pipeline to the cloud, enabling facile use by any researcher without requiring local installation, and parallel automatic annotation of hundreds of genomes.

Finally, we discuss the challenges of scientific analysis of this many genomes, the co-ordination of publications, and the questions that can be answered looking at the genomics of a phylum.