Roland Faure
I'm a PhD student in bioinformatics under the joint supervision of Dominique Lavenier in the Genscale team in Rennes, France and Jean-François Flot and the EBE team at the Université Libre de Bruxelles, Belgium. I love writing fast algorithms processing huge amounts of data, e.g. DNA sequencing data. My area of research is genome assembly and the problem of haplotyping.
Software, publications & talks
Hairsplitter
Separating noisy long reads into an unknown number of haplotypes
Developped under the supervision of Dominique Lavenier and Jean-François Flot
The goal of Hairsplitter is to produce contiguous and uncollapsed (i.e. with all haplotypes still present) assembly. It takes a standard assembly and sequencing reads as input, detects what contigs have been collapsed and output the corresponding uncollapsed assembly. Written in C++. Available on GitHub.
Presented as a poster at Genome informatics 2022 and as a talk at SeqBIM 2022
Graphunzip
Untangling assembly graphs to finish assemblies
Developped under the supervision of Nadège Guiglielmoni and Jean-François Flot
GraphUnzip untangles assembly graphs with the help of long reads and/or Hi-C. It is designed to distinguish the different haplotypes present. Written in Python. Available on GitHub.
Presented the key idea for the first time at JOBIM 2021
The long read algorithm was presented for the first time at SeqBIM 2021 thanks to a grant from the SFBI.
QuickDeconvolution
Rapidly separating barcoded reads into groups
Developped under the supervision of Dominique Lavenier
QuickDeconvolution aims at answering the barcode deconvolution problem when dealing with barcoded reads. It strives at being scalable and parallelisable. Written in C++. Available on GitHub.
Published in Bioinformatics advances
Reviews
NAR Genomics and Bioinformatics
Co-reviewed a paper with Karel Brinda, october 2022
Teaching
Initiation to Java programming
20h of practical sessions with 1st year bachelor computer science students in Rennes 1, Fall 2021
Python object-oriented programming
34h of practical sessions with 1st year master bioinformatics students in Rennes 1, Winter 2022
Educational background
Master "Bioinformatics & modelisation"
Sorbonne universités
Paris, France
Engineering school
École polytechnique
Saclay, France
Math & Physics preparatory school
Lycée Aux Lazaristes
Lyon, France