The Oslo part of the FUGE Bioinformatics platform

CBO and Cigene has for the past year collaborated on developing a cross-breed high throughput SNP-detection pipeline. This is a pipeline for use in sequencing projects, where a large number of traces and clustered sequences are known in a different breed, for instance in genome sequence projects.

The origin for this is the about 152 000 sequences from the Norwegian Red Cattle breed, produced in the bovine sequencing project. A alpha version of the pipeline, written by Eirik Sonneland for his master thesis, is now finished. And a preliminary run gave about 7000 putatitve SNP's, and a rough estimate of the accuracy indicated that about 90% of these SNP's where real.

The pipeline is now being refined, making it more accessible and general. The plan is to make the pipeline general with respect species, make it ready for production and available through the the bioportal.