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 de novo long reads assembly trouble.

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

Talks

  • Correcting Long-Reads with k-mers: A Dream Comes True SeqBim 2020 (pdf)
  • Slides of my PhD defense Novel components at the periphery of long read genome assembly tools (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)

Other Scientific thing