What should we call an overlapping read-pair from a paired-end fragment run?

HiSeq rapid is going to be getting paired-end 250bp reads. Assuming you can sequence with a 500bp insert (+/-50bp) then we can expect to get perhaps 200-300M pairs of overlapping reads that can be merged to create 200-300M 500bp sequences. I suspect this is going to have a transformative effect on genome assembly and transcript isoform detection and the development of novel methods is likely to come from longer and longer reads on the Illumina platforms.

NASA's NextSeq?

A wonderful story appeared on BBC news website today about the company Planet Labs who are using a similar idea Illumina implemented in designing NextSeq - borrow from consumer electronics to advance science. Rather than building sequencers Planet Labs have built and launched a flock of 28 shoebox-sized "cubesats" - cheap, miniature imaging satellites. This is GoogleMaps satellite images with super-high resolution.

DNA technology symposium at Illumina's headquarters in Cambridge

I've just returned from Illumina's 2014 scientific summit in Prague which was a great meeting with loads of interesting speakers, great food (check out this restaurant if you're ever in Prague) and lots of opportunity for engagement with other users as well as Illumina executives. Illumina do put on a good show, so here's details of an event in September.

Say no to DMSO: and remember make your materials and methods clear

DMSO is used in many protocols as a ‘universal solvent’, it’s great for solublising small molecules and you've almost certainly used DMSO when freezing cells or in PCR. Unfortunately it’s relative ubiquity of use in research labs means it’s negative impacts on some compounds can be forgotten. A recent paper in Cancer Research by Michael Gottesman’s lab at NCI highlights one of these: that DMSO inactivates platinum drugs like cisplatin. They demonstrated that DMSO inhibits the cytotoxicity of platinum therapy, and reported that a literature review found up to one third of researchers are using DMSO and make the claim that this may render “a substantial portion of the literature on cisplatin uninterpretable”. Up to 50% of papers did not report the solvent that was used to dissolve cisplatin, making reproducibility of their results potentially impossible.

DMSO inhibits platinum therapy cytotoxicity

Guess which one's the Circos plot

The Circos plot is one of my favourite visualisations of genomic data, it's easy to be blown away by the images our microscopy core produce and genomic data is usually quite a let down by comparison. But the Circos plot is not the first visualisation to use the circular format.

Here are three others: can you spot the Ciros? Answers below.

Choosing an NGS library prep kit provider

Wow there is a lot of choice when it comes to buying something as simple as an NGS library prep kit. With Illumain in mind (as always) I found at least 17 providers. includding: Affymetrix, Agilent, Beckman, Bioo, Enzymatics, Epigentek, Illumina, Kapa, Lucigen, Mclab, Milipore, NEB, NuGen, Qiagen, Rubicon, Swift and Thermo. All these providers offer at least one, if not a whole range, of NGS kits for DNA; and some offer RNA, ChIP, Methlation, etc, etc, etc.

Travel the world with NGS

It's holiday season every season with pretty much every academic pursuit. We're very lucky being ale to escape to some wonderful places to discuss the work we do and face-to-face really is the best way. Sometimes choosing which conference to go to can be a real headache.

AllSeq make this a little easier by presenting a pretty comprehensive list of meetings all over the world in their knowledgbank. And get you a discount too!

Nextera failures fixed by SPRI-cleanup

I'm continuing a series of posts that will highlight small advances we've made in the lab that are unlikely to be published in their own right, this time its the turn of SPRI-bead clean-ups and how we used them to rescue some samples that would not tagment.

The problem: We had a user submit a set of samples for Illumina's rapid exome sequencing in our library prep service. These samples were processed alongside others but the tagmentation for this one user was pretty awful. Most samples dropped out entirely and ony a few generated something that looked as if it had been tagmented at all. The figure below shows tagmentation before SPRI-clean-up and you can clearly see the control (inset) has tagmented and nothing is visible in the second lane where the users samples hold have been. You might also notice that the control is significantly under-tagmented we observed that our control DNA was too high in concentration (15ng/ul instead of 5ng/ul) hence the under tagmentation. Oops!

More of a fizz than a bang: HiSeq 1TB is now available

Updated after a conversation with Illumina: it turns out pricing for V4 was released early in an email from Christian Henry (Illumina SVP & COO) on Feb 25th. Single end pricing is now compared below and list pricing for all reagents has been used in the comparisons of V3 to V4.

Illumina launched the much anticipated v4 kits for 1TB (PE125bp) sequencing on HiSeq 2500 today: we're about to jump from 600GB in ten days to 1Tb in six - awesome and awe inspiring! We are also not far away from 1M reads costing less than 1$!

Turning cancer genomics into an app for your kids phone

Cancer Research UK science has been turned into a game for your mobile: Genes in Space. The aim is to collect space rocks; to do this you need to map a route through the densest regions in space then fly though and catch as many as possible. The great thing is each time you play you're actually navigating through segmented breast-cancer copy-number data from the METABRIC project.