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 to follow the changes of the microbial soil communities over 30 days using shotgun metagenomics. After we have published our paper, I will detail the results of that work at this blog. Here I will just list the tools we used.

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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 of 11 Cod specimens caught in the Oslofjord, Norway.

The Cod in the pilot experiment were wild fish and we had not really an idea what we would find. So it was a bit of a surprise that these 11 fish had only a few species of bacteria in common in their gut. Most species belonged to the order Vibrionales and Bacteriodales. Continue reading

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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 first antibiotics treatment when I was three years old to get rid of a urinary tract infection (UTI). That is now almost 40 years ago. Since then I have had an antibiotics treatment at least once a year to treat chronic or acute infections of the areas connected to my urinary tract system. Continue reading

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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 bunch of software installed, and I then installed the extra software for the course. The software includes MEGAN5, Metaxa2, the metabarcoding tool : obitools, and much more. In addition, I added some tutorial datasets as well. This entire VM is available here.

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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 to only keep contigs larger than 500 bp, but for SPAdes I have not found that restriction. In addition, I did not specify what the coverage cut-off should be in order to keep or thrash low coverage contigs. Continue reading

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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 genome sequences have prophages in I ran two phage finding tools on our selection of genomes: prophinder and PHAST. Both tools gave me different answers for my set of genomes.

With that in mind I decided to test one of the newer tools to identify prophages in bacterial genomes, phiSpy. Here I describe how I installed it on my macbook and how I tested that phiSpy works.

A phage

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Sunlight and shadows

Untitled - nr 1

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 walking woman makes the image more interesting, and when I stood in the lane, I just had to wait until somebody would come walking into the lane for me to capture the moment. I actually had several different shots, but Continue reading

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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 that taking care of my daughter was a full time job with very little spare time. In the end it was better like that.

Nonetheless, I kept on using twitter. Since most of the people that I follow on twitter are working in microbiology or in bioinformatics, I could at least keep myself informed on what was happening in these fields of science.

One of the more interesting things I discovered in that time, was that you can use twitter to update yourself and others on the latest scientific literature. I discovered this through a tweet which pointed me to the blog of Casey Bergman (An assembly of fragments). Casey is the owner of the twitterbot @fly_papers and he described in on of his posts how he set up this twitterbot.

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Where to share data and code… a recent experience.

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

Removing the tag and graffiti. Street art by an unknown artist found in Oslo. Photo by: Thomas H.A. Haverkamp

Removing the tags and graffiti.
Street art by an unknown artist found in Oslo.
Photo by: Thomas H.A. Haverkamp

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

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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.

Electron Micrograph of a typical Thermotogae bacterium: Thermotoga maritima.  The cells ot Thermotogae are surrounded by a membrane called a "toga".

Electron micrograph of a typical Thermotogae bacterium: Thermotoga maritima. Thermotogae cells (dark structure) are surrounded by a membrane called a “toga”, which is the light circle around the cell. Figure by
K.O. Stetter

The data for such analyses comes from DNA shotgun sequencing. A technique were DNA chains are broken up in many small pieces and with sophisticated algorithms the original sequence is retrieved on our computers. In a perfect world we can combine the shotgun sequences into a complete genome sequence without any holes. But as we know, the world is not perfect. Many issues prevent us from creating the original genome sequence of our bug of interest. This blog is an example of what stops us. Continue reading

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