Bioinformatics

Services

Nanuq

FlexArray

Tutorials

Support

SNP discovery and annotation services

One of the common applications of next-generation sequencing is the discovery of novel genetic variants. From a bioinformatics perspective, the first stage is to align the reads on a reference sequence for the species under study. Many tools are available to do this: Bfast, Bowtie (Tophat), mosaik, BWA, Maq and Eland to name a few. The second stage is to feed the alignment information to a SNP caller whose job it is to differentiate sequencing errors from genuine genetic variation. The bioinformatics team has a significant track record with the following SNP callers: Samtools, SNVmix and Gigabayes.

Finally, assuming that the species offers the relevant databases, can annotate the list of SNPs to reflect whether they are novel or not, the genes to which they belong, whether they are synonymous or not. This will greatly improve the classification and the ability to visualize them along other relevant information in a genome browser.

Contact

Bioinformatics Services