Second generation sequencing technologies allow to retrieve billions of sequences for a low price compared to classical Sanger sequencing method. However these sequences have short sizes (a maximum of 300 bases long for Illumina). Today third generation sequencers are now mature enough to produce reads of several kilobases. For functional genomics, long reads could be very usefull for transcriptome analysis as it would allow to directly access isoformes complete sequences in each studied conditons, whereas today only mathematical inferences methods are available to perform this analysis.
École normale supérieure Institute of Biology (IBENS) genomics platform is focus on functional genomics (RNA-Seq and ChIP-Seq) in eukaryotes. It has acquire a MinION seqeuncing device from Oxford Nanopore and wishes to use it to sequence full length transcripts.
The goal of this internship is to develop bioinformatics tools allowing the integration of this new sequencing technology to our RNA-Seq analysis pipeline based on Illumina short reads and to offer to biologists a combination of these two approaches (Illumina and Oxford Nanopore). On the genomic platform we have a long experience on automated and distributed analysis pipelines (Eoulsan and Aozan), using local or distant servers (Cloud computing, calculation grids…). We would like to set up a tool from which the code will be accessible on GitHub and a Docker image to make its installation and usage easy for everyone.
If the Master student is interested by the platform work, it could be possible to pursue after the Master as a bioinformatics engineer on the platform.
We welcome each year one or two students to perform an internship (mandatory or optional). These internships focus either on experimental or bioinformatics aspects of the subjects we are working on at the IBENS genomic platform. If you are interested by our technological approaches, do not hesitate to contact us to submit your application.