kmtricks: efficient and flexible construction of Bloom filters for large sequencing data collections
Bioinformatics Advances Téo Lemane, Paul Medvedev, Rayan Chikhi, Pierre Peterlongo When indexing large collections of short-read...
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Jul 14, 2021
Quicksom: Self-Organizing Maps on GPUs for clustering of molecular dynamics trajectories
Published in Bioinformatics Mallet V, Nilges M, Bouvier G Summary: We implemented the Self-Organizing Maps algorithm running efficiently...
Mar 1, 2021
PanACoTA: a modular tool for massive microbial comparative genomics
NAR Genomics and Bioinformatics Perrin A, Rocha EPC The study of the gene repertoires of microbial species, their pangenomes, has become...
Nov 23, 2020
Cell Tracking Profiler: a user-driven analysis framework for evaluating 4D live cell imaging data
J Cell Sci Mitchell C, Caroff L, Solis-Lemus JA, Reyes-Aldasoro CC, Warburton F, de Chaumont F, Dufour A, Dallongeville S, Olivo-Marin...
Sep 20, 2020
Genuage: visualizing and analyzing multidimensional point cloud data in virtual reality
Nature Methods Thomas Blanc, Mohamed El Beheiry, Clément Caporal, Jean-Baptiste Masson, Bassam Hajj. The quantity of experimentally...
Jul 1, 2020
ARIAweb: a server for automated NMR structure calculation
Nucleic Acids Res Fabrice Allain, Fabien Mareuil, Hervé Ménager, Michael Nilges, Benjamin Bardiaux. Nuclear magnetic resonance (NMR)...
Jun 30, 2020
REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets
Bioinformatics Marchet C, Iqbal Z, Gautheret D, Salson M, Chikhi R. Motivation: In this work we present REINDEER, a novel computational...
Jun 30, 2020
Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing
Brief Bioinform Lima L, Marchet C, Caboche S, da Silva C, Istace B, Aury JM, Touzet H, Chikhi R Motivation Nanopore long-read sequencing...
May 31, 2020
Yacrd and fpa: upstream tools for long-read genome assembly
Bioinformatics Pierre Marijon, Rayan Chikhi, Jean-Stéphane Varré Motivation: Genome assembly is increasingly performed on long,...
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