Monday 23 June 2014

New sequencers from BGI: are they going to take market share from Illumina et al

Everyone knows BGI bought Complete Genomics last year. What is less clear is what BGI's plans are for Complete's platform (a little more at the bottom of this thread). There has also been a bit of buzz about seqeuncers being developed by the genomics institute actually in Beijing. Two recent articles on Chemistry World and Firecebiotechit discuss a newly developed sequencer coming out of the Beijing Institute of Genomics. It may even be in the hands of alpha testers now but my lab is not one of them - BIG: feel free to get in touch!

Thursday 19 June 2014

V4some: 1TB here we come…

Our HiSeq 2500 v4 validation runs are just about to finish and I thought I’d share some details. Ideally I’d give you access to the runs so you can dig around yourselves but until Illumina makes this possible on a per lane basis in BaseSpace you’ll have to make do with my plots.

Tuesday 17 June 2014

Agilent tools to help with your NGS pooling

Pooling samples for multiplexed sequencing has become the norm for many researchers, especially in the light of 1TB sequencing in 6 days! However many users struggle to get pools nicely balanced. I've just seen a tool I think is helpful so I thought I'd share it with you.

Thursday 12 June 2014

Forget the $1000 genome; a house in Cambridge costs more than the 1000 genome project!

I had a chat with a colleague about the insanity of the Cambridge property market and determined that a house here could cost more than the 1000 genomes project. In theory this would cost $1,000,000 if run on HiSeq X Ten today and only take 20 days to sequence, both phenomenal achievements all made possible by the magic Illumina have worked on SBS chemistry.

If only they could magic the Cambridge property market back to somewhere sensible. A Rightmove search in CB3 9HY for houses finds just five available in a 1 mile radius of the number 2 best place to live in the UK. Newnham in Cambridge is a nice place to live offering “country living in the heart of Cambridge”, with a “genuine village atmosphere”, good shops, and good schools. But the cheapest house available is £750,000 or $1,260.000 for 1,407 sq ft, 2 bedrooms and planning for a house in the garden!

Wednesday 11 June 2014

Why no PhiX on BaseSpace: %Q30 vs error rate, should you choose between them

We just had a shiny new NextSeq installed and the validation run gave 480M reads (about 20% above the spec of >400M reads) and 83.1%Q30 (against Illumina's spec of >75%Q30 at 2×150bp). But the initial reaction internally was that the error rates looked too high meaning we were likely trim back to 100bp. The validation run showed error rates of 0.22%, 0.37%, 0.43% at 35, 75 and 100bp respectively, and about 4% at 150bp.