Section: New Results

Experiments with the MinION Nanopore sequencer

Storing information on DNA Molecules

Participants : Dominique Lavenier, Emeline Roux, Ariane Badoual.

In 2019, we started a new research activity aiming to explore the possibility to use the DNA molecules as a storage medium. We designed a complete DNA storage system based on the Oxford Nanopore sequencing technology and performed several experimentations by sequencing several synthetized DNA fragments ranging from 500 to 1,000 bp. These sequences have been designed with ad-hoc coding to prevent specific sequencing errors of the nanopore technology such as indel errors in homo-polymer sequences [29] [34]. These real experiments demonstrate that a text encoded into the DNA alphabet, then synthetized into DNA molecules, sequenced with the MinION, and finally processed using bioinformatics approaches can be fully recovered [28].

Identification of bacterial strains

Participants : Jacques Nicolas, Emeline Roux, Grégoire Siekaniec, Clara Delahaye.

Our aim is to provide rapid algorithms for the identification of bacteria at the finest taxonomic level. We have developed an expertise in the use of the MinIon long read technology and have produced and assembled many genomes for lactic bacteria in cooperation with INRA STLO, which have been made available on the Microscope platform at Genoscope (http://www.genoscope.cns.fr/agc/microscope/). We have developed a first classifier that demonstrates the possibility to identify isolated strains with spaced seed indexing of the noisy long reads produced by the MinIon.