Wednesday 30 April 2014

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.

Monday 28 April 2014

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.

Friday 25 April 2014

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!

Wednesday 23 April 2014

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!

Wednesday 16 April 2014

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$!

Monday 14 April 2014

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.

Monday 7 April 2014

Making ChIP-seq a little more robust

I had a fun time at Jason Carroll's group retreat in sunny Cromer a few weeks ago. I was invited to present some work we'd been doing on using Thruplex for ChIP-seq library prep and there was a lot of great science being discussed.

Tuesday 1 April 2014

MiSeq X: is this Illumina's HiSeq 2500 replacement

Illumina are probably going to announce their latest sequencer today and Core Genomics was heard about it before anyone else...MiSeq X. Similar in name to the HiSeq X Ten the MiSeq X borrows many of the improvements seen in it's big brother including new optics, improved chemistry and a stand-alone server for data analysis allowing upload to BaseSpace. There are fewer restrictions about what we can do on MiSeq X, and the "only Human" has gone.
  • You can buy a single MiSeq X unlike the minimum order of ten HiSeq X's
  • Runs are currently limited to fragment sizes of 350bp but users are not restricted to the TruSeq Nano DNA HT kit, any 350bp library is OK
  • Read length is limited to Paired-End 150bp in the first instance
  • Expect 150M reads per flowcell

What does this mean for HiSeq 2500: It's pretty cool to have a MiSeq that can generate as much data per lane as a HiSeq rapid run, and this creates an interesting problem for potential HiSeq owners. The new MiSeq X uses the same patterned flowcell, chemistry and software advances as the HiSeq X Ten, wrapped up in the form factor of the desktop MiSeq. With the 2x400bp coming by Christmas and assuming the MiSeq X uses all the space in its lane we could get up to 300-400M reads and well over 100Gb per run.

MiSeq X flowcell (courtesy of PowerPoint)

Who's buying MiSeq X: The usual suspects have their machines installed and running; an off the record quote from the Broad said "we got their first, we usually do", and the Sanger said "our history with Illumina means we're usually second, but that's so much better than being last". This is going to be the machine for every other lab outside of the Sanger, Broad and the New York Genome centre (who essentially do everything the Broad does anyway) in their "big-boy" HiSeq X Ten club. Even the BGI are buying these "little-boys".

GenomeWeb contacted both Thermo Scientific (LifeTech) and Complete Genomics for their perspectives:
  • Thermo said "bugger, we're going to get our noses rubbed in those PGM vs MiSeq ads (1, 2, & 3)!"
  • Complete simply replied to their email asking for a response with "我们 投降", which broadly translates to "we surrender"!