Author Archives: Thomas Haverkamp

About Thomas Haverkamp

A microbial ecologist, an amateur photographer and a proud father of a tiny little girl.

A short list of tools for shotgun metagenomics

We are currently finalizing our work on the analysis of metagenomes for soils taken from the Etosha National Park, Namibia. These soils were interesting since Zebra blood containing the nasty bug Bacillus anthracis had poured into it. Our aim was … Continue reading

Posted in Genomics & more, High-throughput Sequencing, Microbes, software | Tagged , , , , , , , , , , | Leave a comment

How many PCR cycles should I use to create an amplicon library?

One of my side projects deals with the gut microbiota of Atlantic Cod (Gadus morhua). In 2014 we published a pilot experiment on this where we sequenced the 16S rRNA to get a taxonomical overview of the microbial gut content … Continue reading

Posted in High-throughput Sequencing, Microbes | Tagged , , , , , , , , , , , | Leave a comment

My antibiotics addiction means trouble for you!

The statement that antibiotics are addictive is of course nonsense, but my experiences with this type of medicine gives me often a different feeling. I will explain why… and get rid of some frustration on the way… I got my … Continue reading

Posted in Microbes | Tagged , , , , , , , , | Leave a comment

Gzip vs Bzip2. Some notes when moving files from Windows 7 to Mac OSX

For a metagenomic bioinformatics course I needed to created a Virtual machine (VM) with all software that will be used during the course. For this I started with the QIIME Virtual machine disk , since it has already a nice … Continue reading

Posted in software | Tagged , , , , | Leave a comment

Removing small & low coverage contigs from a Spades assembly

At the moment I am processing quite a few bacterial genome assemblies that I created for various Thermotogae species. I am comparing assemblies created by CLC, Velvet and the latest SPAdes assembler with REAPR. Both CLC and Velvet were set … Continue reading

Quote | Posted on | 6 Comments

Installing phiSpy on my macbook.

The reason for this post is that in my current project I need to identify prophages in Thermotogales genomes. Prophages are phages /virusses that are integrated into the genome of their host, in our case Bacteria. To check if our … Continue reading

Posted in Genomics & more, Microbes, software | Tagged , , , , , , , , , , , , , , , , , , | Leave a comment

Sunlight and shadows

This photo was taken in the Vigeland park, Oslo on the 7th of june, 2013. It is one of my favourites due to the high contrast, the sun radiating in the trees and the long shadows in the foreground. The … Continue reading

Image | Posted on | Tagged , , , , , , , , , , , | Leave a comment

How to use twitter to follow the latest scientific papers

Last spring I went on parental leave and left science for what it was for more that three months. Writing new posts for this blog was something I thought I could do in my spare time, but soon I realized … Continue reading

Posted in Random stuff | Tagged , , , , , , , | 2 Comments

Where to share data and code… a recent experience.

Today I am writing a rant here since I am quite fed up.

The reason for this post is the following: A paper on which I am a co-author was recently accepted for publication in the journal BMC bioinformatics, after being rejected in BMC genomics since our paper was not suitable for that journal. It’s a bioinformatics tools to analyze big blast files, so that is not bad at all. Such news is wonderful, and as a young scientist these are the moments you work for.

So what is making me fed up? Continue reading

Posted in Publications | Tagged , , , , , | Leave a comment

Is improvement possible? Quality control of a Illumina Nextera dataset for the novo genome assembly

In my current postdoc I work on genome analysis of multiple thermophilic bacteria belonging to the phylum Thermotogae. The data for such analyses comes from DNA shotgun sequencing. A technique were DNA chains are broken up in many small pieces … Continue reading

Posted in Genomics & more, High-throughput Sequencing | Tagged , , , , , , , , , , , , , , , , | 8 Comments