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Fun Opinion

Microbial Advent Calendar – A review

Now that I can move my neck properly again it's time to have a look back on my Microbial Advent Calendar attempt. The exercise was to produce a small blog post a day, for 24 days, about a cool microbiology fact/paper related anywhere from close to pretty far from the…

AdrienJanuary 3, 2018

Bio-informatic [PwD] H. pylori

[Playing with Data] 607 pylori part III: Start digging

Hello Folks, it's been a while! I thought it would be time to continue this big Helicobacter pylori genomes experiment and keep the blog going on. We left with the previous post on preparing the data for our analyses. The main next step will be re-annotating all the genomes in…

AdrienNovember 14, 2017

Bio-informatic Play with Data

[Playing with Data] Looking at a Fish pathogen genome

In this blog note I will use some of the techniques I used in my previous post to look at a recently published dataset. Last year I came across a study by the Institute for Veterinary Pathology, in Zürich, Switzerland describing a bacterial pathogen of fish. Aquaculture is a big…

AdrienSeptember 5, 2016

Bio-informatic

Fetching information from NCBI directly from the command line

I recently (re)discovered the edirect software package published on NCBI. As described on the website this "software suite that enables users to use the UNIX command line to directly access NCBI databases, as well as to parse and format the data to create customized downloads". How does it work? Basically…

AdrienJuly 26, 2016

Bio-informatic

Metagenome part 1 : Getting stuff ready

I am sitting on this blog for too long. I think it is time I try to publish something useful on it. So to do so I am going to present here in a series of short articles how I handle metagenome analyses. I am not pretending to have the…

AdrienDecember 22, 2015

Microbial Advent Calendar – A review

[Playing with Data] 607 pylori part III: Start digging

[Playing with Data] Looking at a Fish pathogen genome

Fetching information from NCBI directly from the command line

Metagenome part 1 : Getting stuff ready

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