Presentation

I am an INRIA PhD student in BONSAI bioinformatics research team at University of Lille 1, France. I study de novo genome sequencing and assembly, with third generation sequencing technology.

Software

  • KNOT: for Knowledge Network Overlap exTraction a pipeline to investigate fragmented long-read assembly
  • yacrd Yet Another Chimeric Read Detector: using all-against-all read mapping for chimeric read detection and read scrubbing
  • fpa 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

Publications

Talks

  • 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