SyntenyViewer

URGI (Unit Resources Genomics-Info) is a bioinformatics facility who support various research activities on plants of agronomic and forestry interest for INRAE. The platform has federated with 3 other INRAE ​​bioinformatics platforms to form the BioinfOmics research infrastructure. It is part of the French Institute of Bioinformatics which is the French node of the European infrastructure ELIXIR . URGI is part of the Saclay Plant Science network and of the Graduate School Biosphera . URGI is labeled by GIS IBiSA and is ISO-9001 certified.

JCVI is a versatile toolkit for comparative genomics analysis. It is a collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.

Tandem repeat genotyping with long reads, being a modified version of HipSTR.

SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods.

Structural variant discovery by integrated paired-end and split-read analysis.

Minigraph is a sequence-to-graph mapper and graph constructor. For graph generation, it aligns a query sequence against a sequence graph and incrementally augments an existing graph with long query subsequences diverged from the graph.