Blog

Precision Medicine – just a thought

Monday 18 July 2016

Recently I enjoyed some poolside time and did some thinking again. The funny thing is that when your mind is no longer directed to the feet of daily work, it starts wandering in all kinds of directions, as if it was not mine. I admit, that I did feed it with the thoughts of Nobel… Read more »

PLANT GENOMICS A SPECIAL BREED OF GENOMICS

Plant Genomics
a special breed of genomics

Thursday 12 May 2016

NGS has rolled out in the area of plant genomics at a rapid pace. However, there are subtle differences between AgBio and human genomics, which do make life of plant researchers more difficult. For instance, the diversity or lack of available reference material puts a much stronger requirement on your tools to use large and complex assemblies for resequencing projects.

NGS QUALITY CONCERNS

NGS Quality Concerns

Friday 18 March 2016

Let’s talk about NGS quality concerns, the data that serves as a foundation for decision-making. Initiatives to get to higher quality levels are manifold. I like to touch briefly on new chemicals, ‘precision’ reference, long reads and population calling.

Rare Disease Day

Rare Disease Day

Monday 29 February 2016

The actuality of today is marked with Rare Disease Day. If you look at the number of places where events are organized to collect monies to finance in depth research this must be a very important topic. The national programs in e.g. Germany to deal with patients with chronic rare diseases ranging from home and clinical care… Read more »

Architecture For NGS Data Processing

Building a Sustainable Architecture For NGS Data Processing

Thursday 18 February 2016

It is not a new phenomenon that the field of genomics must deal with a data processing challenge. Moore’s law and in connection budgets cannot keep up with the increased data processing requirements. The spark to work with new and larger cohorts in NGS studies to increase the ability to find new indicators with higher confidence drives down sequencing cost, yet reaches an IT cost point, which slowly becomes an inhibitor. There is only one-way out: Innovation!

The Genetic Safety Crosscheck

The Genetic Safety Crosscheck

Tuesday 2 February 2016

We pride ourselves in providing high quality output, because one cannot be careful enough, when it gets to health. This does not only apply to humans, but to animals and plants as well. Specifically, when they become part of the human food chain or domicile. Technology is moving very fast and already allows the genetic crosscheck to be engineered at very low cost levels and can easily be conducted at the scale of millions of samples.

From multi-column VCF to GVM

Population Nitro
from multi-column VCF to GVM

Thursday 3 December 2015

As it has been proven that Population Calling, Group Calling or Joint Genotyping has clear advantages, one wonders why this is not being used for all research projects dealing with cohorts of samples. The answer is simple: pain! Or to put it in other words, the resource requirements in terms of compute, storage, network bandwidth,… Read more »

Blessed be the population

Blessed be the Population
from Joint Calling to Population Calling

Thursday 8 October 2015

Today we will bend our minds around the concept and benefits of Population Calling. In the course of recent events this is an obvious choice. Not just because the concept has great potential in health care; being immersed in the subject by releasing a product in this space sort of defines my mindset. We use… Read more »

The Curse of the Format

The curse of ‘The Format’
moving away from the BAM file

Thursday 17 September 2015

As we continue our contemplation on topics that are relevant in our genomics space, we arrive at ‘The Format’ as relevant and important. We discussed the importance of the ‘lossy’ part of any data contained in a format in our first blog “NGS Big Data: Fear and Challenge”. Today we discuss ‘The Format’ itself. There… Read more »

The value of benchmarks

The value of benchmarks
Genome in a Bottle & safety nets

Monday 10 August 2015

In our last blog post “The Quality of Speed” we discussed that embracing new technologies to increase speed and reduce file sizes will move us forward. History consistently shows that these go hand in hand with quality improvements and also contribute to the quality and well-being of both individuals and society. Standards and safety nets… Read more »