86 citations · 151 across the 7 of their papers we have counts for
8 papers
Pattern matching under DTW distance
Garance Gourdel, Anne Driemel, Pierre Peterlongo +1
In this work, we consider the problem of pattern matching under the dynamic time warping (DTW) distance motivated by potential applications in the analysis of biological data produ…
Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs
Antoine Limasset, Jean-Francois Flot, Pierre Peterlongo
Motivations Short-read accuracy is important for downstream analyses such as genome assembly and hybrid long-read correction. Despite much work on short-read correction, present-da…
A resource-frugal probabilistic dictionary and applications in bioinformatics
Camille Marchet, Lolita Lecompte, Antoine Limasset +2
Indexing massive data sets is extremely expensive for large scale problems. In many fields, huge amounts of data are currently generated, however extracting meaningful information…
Fast and scalable minimal perfect hashing for massive key sets
Antoine Limasset, Guillaume Rizk, Rayan Chikhi +1
Minimal perfect hash functions provide space-efficient and collision-free hashing on static sets. Existing algorithms and implementations that build such functions have practical l…
A resource-frugal probabilistic dictionary and applications in (meta)genomics
Camille Marchet, Antoine Limasset, Lucie Bittner +1
Genomic and metagenomic fields, generating huge sets of short genomic sequences, brought their own share of high performance problems. To extract relevant pieces of information fro…
Multiple Comparative Metagenomics using Multiset k-mer Counting
Gaëtan Benoit, Pierre Peterlongo, Mahendra Mariadassou +4
Background. Large scale metagenomic projects aim to extract biodiversity knowledge between different environmental conditions. Current methods for comparing microbial communities f…
Commet: comparing and combining multiple metagenomic datasets
Maillet Nicolas, Collet Guillaume, Vanier Thomas +2
Metagenomics offers a way to analyze biotopes at the genomic level and to reach functional and taxonomical conclusions. The bio-analyzes of large metagenomic projects face critical…
Read Mapping on de Bruijn graph
Antoine Limasset, Bastien Cazaux, Eric Rivals +1
Background Next Generation Sequencing (NGS) has dramatically enhanced our ability to sequence genomes, but not to assemble them. In practice, many published genome sequences remain…