I’m a PhD student in bioinformatics in the Genscale team under the supervision of Pierre Peterlongo and Rayan Chikhi. This thesis project aims to develop bioinformatics method for detection of neurodegenerative structural variants using k-mers matrices. It focus on making the computational tools necessary to scale the concept of k-mers matrices to hundreds whole-genome human sequencing, and propose an implementation of a structural variant detection tool based on this technique. In general terms, I’m highly interested by algorithms and data structures and their applications on biological sequences.
kmtricks is a tool suite for counting kmers, and constructing bloom filters or counted kmer matrices from large and numerous read sets.
- SeqBIM 2020 kmtricks: modular k-mer count matrix and Bloom filter construction for large read collections [slides]
- DSB 2020 HowDeSBT and Simka wedding: what as been done and what we plan to do ? [slides]
- 2019-now: Strings algorithms and bioinformatics, MSc1 Software Engineering, ISTIC