Chromosome-Scale Scaffolds And The State of Genome Assembly →

Keith Robison has written another fantastic post on his Omics! Omics! blog which is a great read for two reasons.

First he looks at the issues regarding chromosome-size scaffolds that can now be produced with Hi-C sequencing approches. He then goes on to provide a brilliant overview of what the latest sequencing and mapping technologies mean for the field of genome assembly:

For high quality de novo genomes, the technology options appear to be converging for the moment on five basic technologies which can be mixed-and-matched.

  • Hi-C (in vitro or in vivo)
  • Rapid Physical Maps (BioNano Genomics)
  • Linked Reads (10X, iGenomX)
  • Oxford Nanopore
  • Pacific Biosciences
  • vanilla Illumina paired end

This second section should be required reading for anyone interested in genome assembly, particularly if you've been away for the field for a while.

Read the post: Chromosome-Scale Scaffolds And The State of Genome Assembly

What did I learn at the Festival of Genomics conference? →

Last week I attended the excellent Festival of Genomics conference in London, organised by Front Line Genomics. This was the first time I had been to a conference as a communications person rather than as a scientist…something that felt quite strange.

In addition to live-tweeting many talks for The Institute of Cancer Research where I work, I also recorded some videos of ICR scientists on the conference floor. All were asked to respond to the same simple question: Why is genomics important for cancer research?. You can see the video responses on the ICR's YouTube channel.

I also made a very short video to highlight one unusual aspect of the conference…the talks were pretty much silent. Wireless headphones worn by all audience members meant that there was no need to amplify the speakers…and therefore no need for the four different 'lecture theatres' to actually have any walls!

 

My first ICR blog post!

My final task was to write a blog post about some aspect of the conference. Before the conference started, I thought I might write something that was more focused on genomics technologies. However, I was surprised by how much of the conference covered genomics as part of healthcare.

In particular, I was left with the sense that genomics is finally delivering on some of the promises made back in 2003 when the human genome sequence was published. One of the target areas that was mentioned in this 2003 NIH press release was 'New methods for the early detection of disease'.

This is something that is now possible with whole genome sequencing being deployed as part of the 100,000 genomes project (undertaken by Genomics England). The ability to screen a patient for all known genetic diseases leads to many concerns and challenges — you should see Gattaca if you haven't already done so — but it was heartening to see how much groundwork has been put in to stay on top of some of these issues.

This is my first proper blog post for the ICR, and if you are interested in finding out more, please read my post on the ICR's Science Talk blog:

We have not yet reached 'peak CEGMA': record number of citations in 2016

Over the last few weeks, I've been closely watching the number of citations to our original 2007 CEGMA paper. Despite making it very clear on the CEGMA webpage that is has been 'discontinued' and despite leaving a comment in PubMed Commons that people should consider alternative tools, citations continue to rise.

This week we passed a milestone with the paper getting more citations in 2016 than in 2015. As the paper's Google Scholar page clearly shows, the citations have increased year-on-year ever since it was published:

While it is somewhat flattering to see research that I was involved so highly cited — I can't imagine that many papers show this pattern of citation growth over such a long period — I really hope that 2016 marks 'peak CEGMA'.

CEGMA development started in 2005, a year that pre-dates technologies such as Solexa sequencing! People should really stop using this tool and try using something like BUSCO instead.

Assembling a twitter following: people continue to be interested in genome assembly

Late in 2010, I was asked to help organise what would initially become The Assemblathon and then more formally Assemblathon 1. One of the very first things I did was to come up with the name itself — more here on naming bioinformatics projects — register the domain name, and secure the Twitter account @Assemblathon.

The original goal was to use the website and Twitter account to promote the contest and then share details of how the competition was unfolding. This is exactly what we did, all the way through to the publication of the Assemblathon 1 paper in late 2011. Around this time it seemed to make sense to also use the Twitter account to promote anything else related to the field of genome assembly and that is exactly what I did.

As well as tweeting a lot about Assemblathon 2 and a little bit about the aborted but oh-so-close-to-launching Assemblathon 3, I have found time to tweet (and retweet) several thousand links to many relevant publications and software tools.

It seems that people are finding this useful as the account keeps gaining a steady trickle of followers. The graph below shows data from when I started tracking the follower growth in early 2014:

All of which leaves me to make two concluding remarks:

  1. There can be tremendous utility in having an outlet — such as a Twitter account — to focus on a very niche subject (maybe some would say that genome assembly is no longer a niche field?).
  2. Although I am no longer working on the Assemblathon projects — I'm not even a researcher any more — I'm happy to keep posting to this account as long as people find it useful.