Some thoughts on today’s Ion World announcements
A few significant announcements from Ion World today (sourced from the press release and #ionworld Tweets) which I’ve summarised here: Proton III and Avalanche The Ion Proton is now shipping and Life Tech plan to ship 100 instruments to customers in September. The initial chip, Proton I (“PI”) will do 60-80m reads and “up to 10Gb” of [...]
Benchtop Sequencer Comparison paper
In case you haven’t seen our recent paper, you can download the paper here (subscription required): http://dx.doi.org/10.1038/nbt.2198 Performance comparison of benchtop high-throughput sequencing platforms Nature Biotechnology advance online publication published online 22 April 2012 Nicholas J Loman, Raju V Misra, Timothy J Dallman, Chrystala Constantinidou, Saheer E Gharbia, John Wain & Mark J Pallen Here is a press [...]
Ion Torrent Proton Announced: The Chip Is (Not) The Machine
Big announcement today from Life Technologies who have announced the Ion Torrent Proton(tm). This, to all intents and purposes is the PGM-2, the second iteration of their pH-meter-on-a-chip sequencing machine. Indeed it is curious they have dropped the Personal Genome Machine moniker, as this product is the first to explicitly target the $1000 (human) genome [...]
2011: Review of a Remarkable Year
2011 has been a remarkable year for me, during which I have travelled widely, met lots of interesting people, recruited substantial grant funding and had a paper published in the journal with the highest impact factor of them all! So, at the risk of producing one of those cheesy round-Robin letters that get stuffed in [...]
Vorsprung durch Technik: talk at Prokagenomics 2011 in Göttingen, Germany
http://youtu.be/HyN2BZPItrg
Vorsprung durch Technik: Talk on Open-source genomics of German E. coli outbreak
A talk given at the University of Birmingham Open Day 10 Sept 2011 Further information on the topics covered in this talk can be found here: http://www.nejm.org/doi/full/10.1056/NEJMoa1106483 (source of figures illustrating epidemiology of outbreak) https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/wiki http://pathogenomics.bham.ac.uk/blog/ http://www.nejm.org/doi/pdf/10.1056/NEJMoa1107643 http://pathogenomics.bham.ac.uk/staff/mpallen.html http://carlzimmer.com/books/microcosm/index.html http://twitter.com/#!/mjpallen http://twitter.com/#!/pathogenomenick
Assessing Ion Torrent assembly quality with Mauve Assembly Metrics
I wanted to assess the quality of the assemblies that you might expect to get from assembling Ion Torrent reads de novo for bacterial genomes (see my last post for the initial results of assembly). By good fortune, Aaron Darling of Mauve fame just published a manuscript in Bioinformatics describing Mauve Assembly Metrics. For those [...]
Ion Torrent: What is the impact of the new longer reads on assembly?
Ion Torrent have released a set of longer read 314 data, along with this technical note. (Graphic from PRINSEQ) The reads are indeed much longer than we have seen with our previous 316 runs, with a mean of 223bp and longest read being 398bp. Curiously this longer-read protocol has been done on a 314 chip [...]
Ion Torrent 316 First Impressions
Last week we had our Ion Torrent upgraded to support the 316 chips at the faster flow rate – many thanks to Life Tech for getting this update to us so quickly. Although Life Tech supply an E. coli K-12 DH10B library for testing (yay, E. coli beats boring old PhiX! BTW is PhiX the [...]