Software | Inception

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...

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...

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...

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...

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...

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)...

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...

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...

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,...