Pierre Marijon picture

Pierre Marijon

PostDoc in bioinformatics

pierre [at] marijon.fr

Presentation

I'm currently part of the research and development team at the SeqOIA diagnostic genetic analysis laboratory. Where I'm working on the problem of interrogating large databases of variants from numerous individuals associated with clinical information. I did a post-doc in Germany in Tobias Marshall's team, where I worked on the detection and phasing of variants using long-reads, as well as on the construction of pangenome. I did my thesis in the BONSAI team, I was supervised by Rayan Chikhi and Jean Stéphane Varré.

My current work focuses on the construction and interrogation of a database of variants containing a large number of individuals associated with clinical signs. I have previously worked on long reads correction and their use for variants detection, de novo genomes assembly, construction and analysis of pangenomes but I'm still depply interested in these matters.

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
  • variantplaner: a toolkit to quering many variants from many samples, with limited resources

Publications

My thesis is avaible on these.fr

Main

Contribution

  • A draft human pangenome reference (Nature)
  • Gaps and complex structurally variant loci in phased genome assemblies (Nature)
  • Cutevariant: a GUI-based desktop application to explore genetics variations (Bioinformatics Advances)
  • 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

  • SAKE: How to fish variants in a data lake at AGHM 2024 congres (pdf)
  • VariantPlaner: Quering many variant without cluster at SFMPP 2023 congres (pdf)
  • 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

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