banner

Ion Torrent Long Read Pilot Projects

EdgeBio is committed to testing and validating the latest technologies from Ion Torrent to provide the latest sequencing services to our clients as soon as possible. Recently we successfully performed some pilot runs using the new long read chemistry. Although we haven't yet achieved the high loading we used to achieve with short read chemistry, we are pleased with the run quality and throughput from our pilot runs and want to share some of the data with the community.

Many of the sequencing runs released so far from Ion Torrent (with the exception of two new HuRef 318 chip datasets available here) have been resequencing of DH10B. While E. coli is a good organism for validation and testing, we see human sequencing as the main Ion Torrent application for us in the future. For this reason we typically run both DH10B and hg19 pilot runs when testing new technology. The run we are releasing today is shotgun resequencing of Craig Venter HuRef DNA. While the mean coverage depth and percent coverage are quite low and aren't really useful for variant calling, the high throughput of AQ20 data from this run shows the Ion's potential for targeted human resequencing.

Tags: 
Posted in: 

snpEff Plugin - Ion Torrent Plugin Development Challenge

In November Ion Torrent announced the “Torrent Suite Plugin Development Challenge” to invite Ion Torrent users to show their programming skills and provide additional functionality for the Torrent Server.   I’d like to take you through our submission to the contest, a plugin that predicts variant effects and annotates vcf files through the snpEff tool.

Predicting variant effects is an important part of an analysis pipeline. By annotating variants it is possible to quickly identify and separate variants based on the predicted effect they will have on associated genes. If an identified variant will result in a gain or loss of a stop codon this variant will likely have a 'high' effect on the gene in which it is located. Conversely, if a variant occurs in an intergenic region or causes a synomous codon change, this variant would have a lower predicted effect.

Tags: 
Posted in: