From reads to transcripts: de novo methods for the analysis of transcriptome second and third generation sequencing.

Camille Marchet 1, 2
2 GenScale - Scalable, Optimized and Parallel Algorithms for Genomics
Inria Rennes – Bretagne Atlantique , IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
Abstract : The purpose of this thesis work is to allow the processing of transcriptome sequencing data, i.e. messenger RNA sequences, which reflect gene expression. More precisely, it is a question of taking advantage of the characteristics of the data produced by the new sequencing technologies, known as third generation (TGS). These technologies produce large sequences, which cover the total length of RNA molecules. This has the advantage of avoiding the sequence assembly phase, which was tricky, though necessary with the data generated by previous sequencing technologies called NGS. On the other hand, TGS data are noisy (up to 15% sequencing errors), requiring the development of new algorithms to analyze this data. The core work of this thesis consisted in the methodological development and implementation of new algorithms allowing the grouping of TGS sequences by gene, then their correction and finally the detection of the different isoforms of each gene.
Keywords : Bioinfomatics
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Theses
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Camille Marchet. From reads to transcripts: de novo methods for the analysis of transcriptome second and third generation sequencing.. Bioinformatics [q-bio.QM]. Université de Rennes 1, 2018. English. ⟨tel-01939193⟩

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