Structure Content

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 […]

Chromosomes of all species studied so far display a variety of higher-order organizational features such as domains, loops, or compartments. Many of these structures have been characterized from the genome-wide contact maps generated by […]

Scans a set of protein sequences for type IV secretion systems and relaxases using HMM profiles. See Guglielmini et al. (2011) for our criteria to class loci on the basis of this output. Except […]

COV2HTML is an interactive web interface, which is addressed to biologists, and allows performing both coverage visualization and analysis of NGS alignments performed on prokaryotic organisms (bacteria and phages). It combines two processes: a […]

The CRISPRCasFinder program enables the easy detection of CRISPRs and cas genes in user-submitted sequence data (allows sequences up to 50 Mo otherwise download standalone program). This is an update of the CRISPRFinder program […]

A software to reconstruct 1D genome structures from 3D contact data obtained from Hi-C experiments. This movie shows the iterative assembly by GRAAL of the Trichoderma reesei genome (right) using contact frequencies determined by […]

Growthpred predicts bacterial minimal doubling times by analysing codon usage bias in genomes and metagenomes. The program takes a set of DNA protein coding sequences, searches for ribosomal protein coding genes and translates all […]

https://github.com/koszullab/instaGRAAL Hi-C exploits contact frequencies between pairs of loci to bridge and order contigs during genome assembly, resulting in chromosome-level assemblies. Because few robust programs are available for this type of data, we developed […]

IntegronFinder is a program that detects integrons in DNA sequences. The program is available on a webserver (Galaxy), or by command line (IntegronFinder on github). It is now in its second version. Integrons are […]

Macromolecular System Finder (MacSyFinder) provides a flexible framework to model the properties of molecular systems (cellular machinery or pathway) including their components, evolutionary associations with other systems and genetic architecture. Modelled features also include […]

https://github.com/koszullab/metaTOR We have pushed further our analysis about the potential of 3D contact data to solve genomics limitations and problems. We have developed meta3C, a metagenomic chromosome conformation capture approach that allows characterizing individual […]

The study of the gene repertoires of microbial species, their pangenomes, has become a key part of microbial evolution and functional genomics. Yet, the increasing number of genomes available complicates the establishment of the […]

Bacteriophages are the most abundant viruses on earth and display an impressive genetic as well as morphologic diversity. Among those, the most common order of phages is the Caudovirales, whose viral particles packages linear […]

Repeatoire is a bioinformatics tool for locating DNA repeats inside of sequenced (but not necessarily assembled) genomes. Specifically, our focus is on repeat families, i.e. related sets of repeats that share a similar role […]

While there were efficient methods for detecting strict repeats or detecting already characterised repeats, there was no software available for detecting approximate repeats in large DNA sequences allowing for weighted substitutions and indels in […]

SARTools is a R package dedicated to the differential analysis of RNA-seq data. It provides tools to generate descriptive and diagnostic graphs, to run the differential analysis with one of the well known DESeq2 […]

Bacteriophage–bacteria interactions are affected by phage satellites, elements that exploit phages for transfer between bacteria. Satellites can encode defense systems, antibiotic resistance genes, and virulence factors, but their number and diversity are unknown. We […]

Sequana is a Python framework designed to provide pipelines to analyse Next Generation Sequencing data sets. Sequana provides tools to access the sequence quality but also post-processing analysis such as depth of coverage or […]

We designed a PyQt graphical user interface—Sequanix—aimed at democratizing the use of Snakemake pipelines in the NGS space and beyond. By default, Sequanix includes Sequana NGS pipelines (Snakemake format) (http://sequana.readthedocs.io), and is also capable […]

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7320618/ Motivation: Hi-C contact maps reflect the relative contact frequencies between pairs of genomic loci, quantified through deep sequencing. Differential analyses of these maps enable downstream biological interpretations. However, the multi-fractal nature of the […]

SHAMAN is a SHiny Application for Metagenomic ANalysis including the normalization, the differential analysis and mutiple visualization. SHAMAN is based on DESeq2 R package [Anders and Huber 2010] for the analysis of metagenomic data, […]

Intragenic duplications of genetic material have important biological roles because of their consequences in terms of protein sequence and structure. We developed Swelfe to find internal repeats at three levels. Swelfe quickly identifies statistically […]