Alexis Criscuolo

Neonatal acquisition of ESBL-PE in the community of a Low-Income Country  Severe bacterial infections are a leading cause of neonatal deaths, with low income countries (LICs) bearing the highest burden. In LICs, neonatal bacterial […]

Genotyping method such as microsatellites and MultiLocus Sequence Typing (MLST) are frequently used to confirm the link between isolates responsible of invasive infections. But these methods are only available for frequent fungal species. For […]

The protozoan parasite Leishmania donovani causes fatal visceral leishmaniasis, one of the most neglected tropical diseases. In the absence of economic incentive, serious Research and Development (R&D) investments into anti-leishmanial drug development lack from […]

High-throughput sequencing has revolutionized our abilities to track and characterize novel bacterial strains as they emerge and disseminate globally. Genome-based epidemiological typing systems provide ultimate resolution for strain discrimination. Genome sequences may also be […]

The Institut Pasteur has voluminous activities of microbial strain characterisation, in the context of epidemiological surveillance, biological resource centres collections management, and research. These activities involve National Reference Centers, WHO-collaborative centers, biological resources centers […]

BIGSdb-Pasteur is the genomic-based strain taxonomy and nomenclature platform of Institut Pasteur, powered by the BIGSdb software developed at Oxford University. This web platform hosts collections of curated, open or private databases of bacterial […]

Due to advances in high-throughput sequencing technologies, generating whole genome sequencing (WGS) data with high coverage depth (e.g. ≥ 500×) is now becoming common, especially when dealing with non-eukaryotic genomes. Such high coverage WGS […]

JolyTree implements an alignment-ƒree distance-based procedure ƒor inferring phylogenetic trees ƒrom genome contig sequences. For each pair of genomes, a dissimilarity measure is ƒirst computed and next transƒormed to obtain an estimation oƒ the […]

Contaminant oligonucleotide sequences such as primers and adapters can occur in both ends oƒ high-throughput sequencing (HTS) reads. AlienTrimmer was developed in order to detect and remove such contaminants. ßased on the decomposition oƒ […]

The quality of multiple sequence alignments plays an important role in the accuracy of phylogenetic inference. It has been shown that removing ambiguously aligned regions, but also other sources of bias such as highly […]

fq2dna (FASTQ files to de novo assembly) is a command line tool to ease the de novo assembly oƒ archaea, bacteria or virus genomes ƒrom raw high-throughput sequencing (HTS) paired-end (PE) reads. Every data […]

ƒqCleanER (ƒastq Cleaning and Enhancing Routine) is a command line tool to ease the diƒƒerent standard preprocessing steps oƒ short high-throughput sequencing (HTS) reads. Eight standard HTS read processing steps can be carried out […]

RΕQ is a program ƒor quickly estimating a conƒidence value at each branch oƒ a distance-based phylogenetic tree. Branch support assessment is commonly based on bootstrap procedures (e.g. Felsenstein 1985, Makarenkov et al. 2010, […]