Hello, my name is Christophe Klopp,
and I will explain what Sigenae is.
Sigenae is a platform of engineers,
which was set up
20 years ago,
and which provides services to biologists
interested in farm animals at INRAE.
These engineers are located on two sites,
as shown on the map,
and belong to 4 departments:
Animal Genetics (GA),
Animal Physiology and Breeding System (PHASE),
Animal Health (SA) and
Mathematics and Numeracy (MathNum).
What services does Sigenae provide?
First of all, the first service,
which corresponds to most of our working time,
is the processing of massive data,
mainly from 2nd and 3rd generation sequencers.
And in terms of applications,
we are focused on variant calling
from genomes or pieces of genomes or even transcriptomes,
on the assembly (genomes or transcriptomes),
we do diversity research (16S),
we perform a lot of expression analysis, expression quantification.
We store genotypes and variants, and perform small RNAs analyses.
We participate in major projects,
such as the 1000 bovine genomes or VarGoats,
we have assembled the bee
or many fishes (in progress).
Another part of our activity is the development of
software and databases.
I have put two examples of software
here on the slide: jVenn and D-Genies.
JVenn is a software which allows you
to make Venn diagrams from lists
and D-Genies is a software which
compares genomes and presents dotplots.
And I have also added the PhyloFish database,
which is a database of transcriptomes of 20 fishes
on 10 tissues, allowing you to
visualise transcripts, annotations
and variants in these transcripts.
It is a rather rich database.
The third part of our activity is training.
We are trainers in the Genotoul bioinfo training courses,
we work on calling variants
as well as on the RNAseq and then
on the various assembly modules.
Sigenae also maintains the Galaxy environment
for the Genotoul community.
We administer the machine, manage the tickets...
And in conclusion: what can Sigenae do for you?
Discuss your projects,
discuss techniques,
train you in bioinformatics and
help you with data processing.
Thank you, see you soon.