Ettema lab blog

Courtney Stairs joins Ettema-lab

One more member joins the Ettema-lab: Courtney Stairs. Courtney did her PhD at Dalhousie University (Halifax, Canada) and recently joined Ettema-lab to investigate the diverse protist biology using single-cell genomics and transcriptomics. In collaboration with Prof. Staffan Svard, she will compare the transcriptomes of the fish pathogen Spironucleus salmonicida in order to identify key adaptations that permit Spironucleus invasion. Welcome Courtney,

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Ettema-lab has a new member

Hej all, first of all let me shortly introduce myself. My name is Martha and I joined Ettema-lab in May 2016 as project coordinator and person for anything administrative (with some lab-work on the side). That also includes joining the team that takes care of our webpage. So be ready for some changes and updates in the future! And

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Multithreading with BLAST

The NCBI BLAST+ suite has built in multithreading, which is nice. However, this multithreading is not always utilising all threads available to it. A nifty way around this is to split your input query into several smaller files (equal to the number of threads you have available) and blast them separately using a single thread

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Simple command line data manipulation

Recently I found a nice little tool called datamash. This allows for simple data wrangling, or should one say mashing, directly on the command line. I found this tool since I wanted to have a way of easily transposing tab separated files via the command line. One such example would be if you have a

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Printing from commandline

When you have a lot of documents to print, perhaps a bunch of papers you want to read, it can be a bit annoying to print these one by one. A nice solution can instead by to do this from the commandline. The ‘lp’ tool is quite nice and can be modified to do a

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New paper about the Hadesarchaea published!

The Ettema-lab has published a new paper about the discovery of a new group of archaea, the Hadesarchaea. This paper, which was the result of a collaboration with Brett Baker’s lab at UTexas (USA), describes the first characterization of the genomes of a group of archaea formerly known as SAGMAG. These archaea were first discovered in 3-kilometer deep gold mines in South-Africa,

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Movie about the research at the Ettema-lab

Part of the research in the Ettema-lab is being funded by the Swedish Foundation for Strategic Research (SSF, http://stratresearch.se/). As part of the ‘Future Research Leader’ program of which Thijs is part of, a short feature film was made about the ongoing research in the Ettema-lab. This week, this film was published on Youtube: /TE

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Julian Vosseberg joins the Ettema-lab

This week, the Ettema-lab has expanded again: Julian Vosseberg, MSc student at Utrecht University (The Netherlands) has joined us to work on an exciting project under supervision of PhD student Joran Martijn. Together they will look at metagenomic datasets to find clues about the elusive origin of the mitochondria, the powerhouse of eukaryotic cells. Welcome Julian, and

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MEGAN5 – need to add auxiliary mapping files

While trying to use MEGAN5 recently (version 5.11.3) noticed that most genes were not being mapped to KEGG/SEED categories. Turns out that the built-in reference maps for KEGG and SEED are now out-of date and you need to supply auxiliary mapping files when importing from a blastp file (blasted using recently updated versions of NCBI’s

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Ebba Bergman joins the Ettema-lab

This week, our lab has expanded yet again: Ebba Bergman joined us! Ebba is a Master student from the ‘X-program’ (Engineer program in Molecular Biotechnology) from Uppsala University, and she will work on building efficient bioinformatics pipelines for efficient analyses of large amounts of next-generation sequencing data. Welcome Ebba!   /TE

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