Presentation

I am currently a post-doc in Tobias Marshall's team. I did my thesis in the BONSAI team, I was supervised by Rayan Chikhi and Jean Stéphane Varré.

My work focuses on long reads correction and their use for variants detection, de novo genomes assembly, construction and analysis of pangenomes.

Software

  • KNOT: for Knowledge Network Overlap exTraction a pipeline to investigate fragmented long-read assembly
  • yacrd: for Yet Another Chimeric Read Detector: using all-against-all read mapping for chimeric read detection and read scrubbing
  • fpa: for Filter Pairwise Alignment: filter all-against-all read mapping, by type, length, name… fpa can convert alignment in overlap graph (GFA1), index and rename reads
  • ragroc: for Random dnA Generator and Reverse COmplement: a webpage write in webassembly to generate random dna and run reverse complement
  • niffler: is a rust crate to provide simple and transparent support for compressed files

Publications

Main

Contribution

  • Cutevariant: a GUI-based desktop application to explore genetics variations (biorxiv)
  • Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads (Nature Biotechnology)
  • A Graph-Theoretic Barcode Ordering Model for Linked-Reads (WABI 2020)

Talks

  • Correcting Long-Reads with k-mers: A Dream Comes True at SeqBim 2020 (pdf)
  • Novel components at the periphery of long read genome assembly tools slides of my PhD defense (pdf)
  • Graph analysis of fragmented long-read bacterial genome assemblies, at RECOMB-Seq 2019 (pdf)
  • Optimizing early steps of long-read genome assembly at Seqbio 2018 (pdf)
  • Debugging long-read genome assemblies using string graph analysis at Seqbio 2017 (pdf)

Review

For journal:

Other Scientific thing