metagenome

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

Metagenome part 3: Binning the reads – the easy part

In the previous article we assembled a first version of the metagenome, using a fast assembler creating a lot of rather small contigs. We need now to separate these reads according to the different genomes present in the assembly: this is called binning. To tease apart the different genomes we…

AdrienJanuary 7, 2016

Bio-informatic

Metagenome part 2: Assembling the reads

We continue the analysis of a metagenome library coming from a sample of the dorsal tongue of SRS147120. After the previous article we now we know what to expect in the metagenomic library. We have quite a diversity of predicted OTU. It is time to do the first round of…

AdrienJanuary 3, 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

[Playing with Data] Looking at a Fish pathogen genome

Metagenome part 3: Binning the reads – the easy part

Metagenome part 2: Assembling the reads

Metagenome part 1 : Getting stuff ready

Interesting Publication