NGS Expert Blog

The High-Throughput Sequencing map by James Hadfield (Cancer Research UK, Cambridge) gives us a very interesting overview about sequencing activities around the world. We ran a survey to find out if your favourite machines correspond with the platforms listed by James in his overview.

Here are the results: Your personal favourites are nearly a perfect match with platforms in the genome centers worldwide. Great match!

Mid of March we wrote about the British Ash Tree Genome Project.

Yesterday, the School of Biological and Chemical Sciences, Queen Mary University of London launched a website explaining in detail their amazing project: Find there general information, data and tools. Further, an interview on the project from the Radio 4 Today programme on 21/12/12 can be heard here. More details on the project can be heard on NERC’s 5/2/13 Planet Earth podcast.

Visit http://ashgenome.org

To conduct genome sequencing and analysis of Ash (Fraxinus excelsior), researchers in the UK received £2.4 million ($3.6 million / €2.8 million). The major aim of this project is to increase the understanding of the wide spreading fungal tree disease, which is widespread in northern Europe and has already been found at more than 300 sites across the UK (see http://www.forestry.gov.uk/chalara). Those fungi attack ash tress but some tress resists those attacks.

For this reason a lot of samples of the ash dieback fungus will be sequenced and – funded by an urgency grant from the Natural Environment Research Council – the complete genome sequence of Ash is aimed to be available by August.

Sequencing of the approximately 900 Mb plant genome will be performed applying the latest hybrid de novo sequencing strategy, recently proven to deliver excellent scaffolding and assembly results. This new golden standard in de novo sequencing employs a combination of Roche/454 FLX++ long read technology (software version 2.8 with read lengths up to 1,100 bp) and Illumina HiSeq 2000/2500 high throughput sequencing with several ultra-accurate long jumping distance libraries (LJD of 3kb, 8kb, 20kb and 40kb), supplemented by sequencing of Illumina shotgun libraries with different fragment sizes.

With the sequenced ash tree genome the researchers hope to hold clues to how some of the trees (2% are able to defend the disease) are able to resist attack, and knowledge about the genetic differences between resistant and non-resistant trees. This knowledge could be used to develop trees that can’t be infected.

Project leader, Dr. Richard Buggs from Queen Mary’s School of Biological and Chemical Sciences: “Sequencing the ash genome is a foundational step towards discovering the genetic basis of resistance to ash dieback – the future of ash trees in Britain may depend on this”.

Read more about that exciting project at GenomeWeb about the general project and at Eurofins MWG Operon about the genome sequencing.

The Genomics Virtual Lab (GVL) project – using the computing resources from the NeCTAR Research Cloud – is an Australian Government project conducted as part of the “Super Science” initiative. It is developing infrastructure supporting genome informatics research.

Their Galaxy-based NGS and HTS tutorials are really excellent:

• RNA-seq tutorial
• Variant detection tutorial
• Variant detection (advanced) tutorial
• Genome assembly tutorial

You will love the precise explanations, the hands-on demonstration and the additional material like screenshots and in-depth information!

the last weeks you were asked for your opinion about the NGS Expert blog. We really were overwhelmed when we have read your comments and positive feedback.
Thank you so much for your interest in reading our blog posts.
We absolutely take your feedback to heart and try to focus on your favourite topics. You are the reason why we keep on reasearching to write exciting blog posts!

Best regards
your NGS Expert team

Discover 2270 high-throughput sequencing machines in 830 centres at http://www.omicsmaps.com/. Select according to a specific platform or search for a facility or a region of your interest. Relevant statistics are also available at http://www.omicsmaps.com/stats.

No matter if you are a commercial service provider, a researcher or a device manufacturer, you will love the map!

Watch out the presentation of the SITN Boston talking about whole genome sequencing and its impact on personalised medicine.

Further recorded lectures given by graduate students at Harvard and focusing on hot topics in science research and news can be found at https://sitn.hms.harvard.edu/seminar-archive-2012/. Enjoy!

Do you know the blog of the Wellcome Trust Sanger Institute?

The Wellcome Trust Sanger Institute is one of the leading genomic research centres in Europe and a leader in the Human Genome Project. Within their blog they are talking about the role of genetics in health and disease by using the latest genomic and genetic techniques.

Read more at http://sangerinstitute.wordpress.com/

We asked for your opinion if it is possible to directly compare the benchtop sequencers MiSeq and IonTorrent with each other. The result was pretty interesting because the 34 votes were distributed nearly evenly.