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Siegfried Dubois

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I am a second year PhD student in bioinformatics, currently working on pangenome graph comparison and representation; located in the GenScale research team at INRIA Centre Rennes-Bretagne, in France.

Conferences

  • SeqBim 2023 & DSB 2024 - Towards an edit distance between pangenome graphs.
  • MIGGS 2024 - Interfacing pangenome graphs using pancat.

Papers

  • Pairwise graph edit distance characterizes the impact of the construction method on pangenome graphs. Siegfried Dubois, Claire Lemaitre, Matthias Zytnicki and Thomas Faraut. bioRxiv 2024.12.06.627166.

SOFTWARE

Main developper
  • rs-pancat-compare. Compute an edit distance between pangenome graph using segmentation.
  • rs-pancat-paths. Execute querries on the paths of a GFA file (pangenome share indices, anchor nodes, fasta extraction...).
  • py-pancat. Proof-of-concept toolkit and visualisation tool (for graph edit distance) to handle GFA graphs.
  • gfagraphs. Python library to manipulate GFA files, load, save, create a coordinate system, edit the graph...
  • sharepg. Proof-of-concept analysis of shared parts in a pangenome.
  • wisp. Metagenomic families assignment using a hierarchical decision trees approach on small k-mers.
Contributor
  • INVPG. Tool to annotate inversions from pangenome graph bubbles.
  • awesome-pangenomes. List of software for pangenomics.

Other

Teachings

2024-2025
  • Oriented-Object Programming, Master 2
  • Structured Data, Licence 2
  • Introduction to Java, Licence 1
2023-2024
  • Introduction to Java, Licence 1
  • Student project, Licence 1