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.

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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. Read the rest of this entry »

Last Wednesday I had the privilege of giving a talk at a local Ion Torrent user group meeting. As one of the more experienced Ion Torrent users in the region EdgeBio was asked to give a summary of a few Ion Torrent applications that we have been working on recently.  I talked a bit about our earlier Variant Calling blog post, talked a bit about our experiences with the IonSet early access barcodes, and presented some new data provided by Ion Torrent showing the Long Range Mate Pair capability on the Ion.  The mate pair protocol was recently released and the data we presented is from a run with average 10kb inserts.  The data was split with the sff_extract utility, mapped both with bwa and tmap, and an average insert size histogram was created.  We found that the data mapped well with a tight distribution around 10,000 bp insert sizes.  This is a really promising result and we are excited to try the mate pair protocol for ourselves.  We’re particularly excited to see these long range mate pairs be extended out to possibly 40kb inserts, which would make the Ion Torrent platform a reliable and affordable method for haplotype phasing in human sequencing.  You can see the slides from the presentation below.

With the announcement of the new RecognitION program EdgeBio is proud to release our latest run of DH10B resequencing data to the community.  Our latest run, using OneTouch prep, yielded 414.31MB (350.93MB Q20) of sequencing data.  We’re really excited to push the platform to its limits and hope that releasing data to the community will help others do the same.

You can view the run report in any web browser by clicking on the link below using the username ‘edgecommunity’ and leaving the password blank:

http://bit.ly/eb_onetouch

The data can also be accessed through the EdgeBio SFTP Data Delivery Server. Access data.edgebio.com over port 22 using the username edgecommunity. No Password is required.