This week I attended porecamp at the University of Birmingham focused on the use of the MinION nanopore sequencer. The workshop was hosted by Nick Loman and included interactive sessions with Matt Loose, Mick Watson, Josh Quick, John Tyson, Justin O’Grady and Jared Simpson. So pretty much every aspect of nanopore sequencing, from library preparation to assembly polishing was covered. Below a brief overview of the activities that were going on, a detailed account will soon be written up in a F1000 article by the participants.
Everyone had the opportunity to bring some DNA samples to try in the new ‘native barcoding protocol’. This pre-release protocol allows for the pooling of multiple samples on one flow cell by, in an extra ligation step, attaching a barcode to the individual samples. The initial results looked pretty good in the sense that it should be possible to obtain an equal distribution of DNA from a pooled library. It also became evident that the use of high quality DNA improves the output from the MinION. When working with genomic DNA the best strategy is to start with a fresh culture, directly phenol-chloroform extract and don’t freeze the DNA before the library prep.
Josh explaining the library prep protocol
John Tyson and Matt Loose thoroughly demonstrated the use of software add ons to improve the process. Johns scripts optimize the way the sequencer selects the correct pore to sequence from and Matt his minoTour software let you realtime analyse the data as it comes of the sequencer, he also showed some pretty cool initial results of the read-until feature, for example to balance the reads of a pooled sample.
Matt performing a -1 G nanopore run
On the bioinformatics side we gave, after diving into the fast5 file format, the new mapper from Heng Li miniasm a try, resulting in very rapid genome assembly. It will be interesting to see how miniasm will find its way into the assembly pipelines.
Concluding this was an extremely valuable week to get to know everyone and exchange knowledge on the latest practices in the nanopore sequencing world. So again a big thanks to the perfect organization.
The course material is available on github and additional information can be found on twitter under #porecamp