The Long-read sequencing technology proposed by ONT (Oxford Nanopore Technologies) is based on the detection of a differential current as a single linear molecule passes through a biological nanopore anchored in a synthetic membrane. The nanopore is an ion flow sensor that varies according to the steric hindrance of the compound passing through it, which allows to identify the sequence of a DNA strand over a large length (up to several Mb) whatever its composition in repeated elements, GC-rich or methylated regions.
This type of sequencing technology can be used in many biological applications (not exhaustive):
- Basic research in genomics:
- Resolve difficult to sequence regions (i.e. repeats) with ultra long reads.
- Identify RNA/DNA chemical modifications (methylation, acetylation) by direct sequencing.
- RNA research
- Characterize and quantify complete transcripts using long reads (direct exon connectivity).
- Explore epitranscriptomic modifications with direct RNA sequencing.
- Clinical research
- Mapping complex structural variants (SV), including insertions of transposable elements.
- Phase the variants using long readings.
- Microbiome
- Assembling complete genomes.
- Sequencing at the sampling location (taking into account portability)
IGDRion Project: MinION@IGDR
This project aims to summarize information about the process of using MinION sequencing technology at IGDR.
We are organized with :
- a GitHub public repositories for tools used/developed by the team: https://github.com/IGDRion
- a GitLab private repo for following projects : https://gitlab.com/bioinfog/nanopore
Localization :
The minION is located on the Villejean Campus, Building 4, IGDR, room 015 (ground floor).
System :
We have
- 2 MK1B e.g. MinION (with one in collaboration with Dominique Lavenier et Emeline Roux).
- 1 MK1C.
- 1 GridION through a loan from a Cancéropôle Grand Ouest project (in collaboration with Drs David Gilot, Aurélien Sérandour et Pierre-François Carton).
