Algorithms and software for third generation RNA sequencing

   sequencer alternative
	 splicing genes


The research projet ASTER is funded by the French National Research Agency (ANR-16-CE23-0001) for the period 2016-2020.

Third generation sequencing is an emerging technology that promises to give a better picture for studying genomes, transcriptomes, metagenomes and metatranscriptomes of all living organisms. It will be key for discovering new fundamental mechanisms in cell biology, with broad implications in environmental research, health and agriculture.

In this project, we will focus on RNA sequencing. The goal is both to evaluate this new technology and to develop innovative and efficient algorithms for analyzing this data. We will consider several settings, depending on whether a reference genome and/or supporting second generation data are available. This will give raise to a number of specialized algorithms in several primary analysis steps that complement one another: alignment, error correction, identification of gene structures, identification of variants.

All sequencing data and algorithms produced during the project will be made publicly available through read archives and open-source software.

Keywords: computational biology, nanopore sequencing, RNA and alternative splicing, metagenomics