GYDLE

Solutions for Genomics

Fr

Innovative Technologies and Analysis Methods

Gydle develops a new generation of bioinformatics technologies for genomic research in health, agriculture, forestry and environmental sciences. Our innovations help scientists leverage the latest DNA sequencing advances and better represent and analyse genomes to accelerate their discoveries. Gydle innovations are featured in numerous publications.

DNA Sequence Alignment

NUCLEAR is a universal tool for aligning, masking and filtering DNA and RNA sequences of any technology and length, from oligos and short reads to gene transcripts and multi-gigabase genomes. NUCLEAR can perform a wide array of tasks including quality filtering, complexity masking, similarity searches, read mapping, repeat finding, gene annotation and whole-genome alignments. Based on a unique multi high-scoring-pair (HSP) model accurately dealing with gaps and multiple mappings, NUCLEAR can align widely divergent sequences while accurately determining the best hit, allowing the analysis of sequences across populations and species.

Genome Assembly & Finishing

Our genome assembly solutions cover the complete continuum between de novo and reference-initiated assemblies and between targeted and whole-genome approaches.   Our unique hybrid assembly algorithms enable the simultaneous use of sequencing, single-molecule and mapping data to construct pseudomolecules representing entire chromosomes with cross-validation of all the supporting data. With capabilities such as iterative assembly improvement, version tracking, integration with finishing, annotation and visualisation modules, our assembly solution enables the construction of genome representations of any size with finished quality regions.

Physical & Optical Mapping

Our complete solution for physical and optical mapping data includes a proprietary optical aligner and assembler, tools for assembling BAC sequencing data, and a visualisation/edition solution, allowing users to curate and improve on BioNano and physical maps and raw single-molecule data and to build complete chromosome pseudomolecule assemblies integrating physical mapping, optical and sequence data.

Visualisation of Genomic data

VISION allows both the visualisation and the edition of genomes, assemblies, alignments, annotation and variants. Based on a powerful graphics engine able to represent very large data sets with publication-quality graphics,VISION integrates our other analysis components as plug-ins in a user-friendly way. VISION is the tool of choice to represent genomes of any size from viruses, bacteria and organelles to multi-gigabase genomes with billions of aligned fragment reads, as well as transcriptomes, pan‑genomes and population datasets.

Universal Genome Storage

GYM is an efficient solution for the storage of genomes, transcriptomes and associated data, including sequence assemblies, aligned fragments, genome maps, annotation and genetic variants. GYM supports multiple categorisations and enables version tracking and dynamic remapping of alignments and features, allowing scientists to collaborate through projects with evolving genome representations. GYM can store whole-genome alignments and relationships, allowing the study of pan‑genomes and comparisons across populations, species and genera.

Variants & Haplotypes

Our variant analysis software identifies SNPs, indels and structural variants with high-accuracy using both DNA‑Seq and RNA‑Seq data. Combined with our uniquely accurate NUCLEAR fragment mapping software, it can perform variant discovery and genotyping simultaneously across thousands of individuals, reconstruct haplotypes for any ploidy model, and classify variants according to their sequence context.

Gydle develops a new generation of analysis tools to accelerate genomic research in health, agriculture, forestry and environmental sciences. Leveraging the latest DNA sequencing and single-molecule technologies, our novel bioinformatic algorithms and cutting-edge software help scientists better represent and analyse genomes, leading to enhanced discoveries in pharmaceutical, breeding, functional genomics, systematics and evolutionary studies. Gydle innovations are featured in numerous publications.

NUCLEAR is a universal tool for aligning, masking and filtering DNA and RNA sequences of any technology and length, from oligos and short reads to gene transcripts and multi-gigabase genomes. NUCLEAR can perform a wide array of tasks including quality filtering, complexity masking, similarity searches, read mapping, repeat finding, gene annotation and whole-genome alignments. Based on a unique multi high-scoring-pair (HSP) model accurately dealing with gaps and multiple mappings, NUCLEAR can align widely divergent sequences while accurately determining the best hit, allowing the analysis of sequences across populations and species.

Our genome assembly solutions cover the complete continuum between de novo and reference-initiated assemblies and between targeted and whole-genome approaches.   Our unique hybrid assembly algorithms enable the simultaneous use of sequencing, single-molecule and mapping data to construct pseudomolecules representing entire chromosomes with cross-validation of all the supporting data. With capabilities such as iterative assembly improvement, version tracking, integration with finishing, annotation and visualisation modules, our assembly solution enables the construction of genome representations of any size with finished quality regions.

VISION allows both the visualisation and the edition of genomes, assemblies, alignments, annotation and variants. Based on a powerful graphics engine able to represent very large data sets with publication-quality graphics, VISION integrates our other analysis components as plug-ins in a user-friendly way. VISION is the tool of choice to represent genomes of any size from viruses, bacteria and organelles to multi-gigabase genomes with billions of aligned fragment reads, as well as transcriptomes, pan‑genomes and population datasets.

GYM is an efficient solution for the storage of genomes, transcriptomes and associated data, including sequence assemblies, aligned fragments, genome maps, annotation and genetic variants. GYM supports multiple categorisations and enables version tracking and dynamic remapping of alignments and features, allowing scientists to collaborate through projects with evolving genome representations. GYM can store whole-genome alignments and relationships, allowing the study of pan‑genomes and comparisons across populations, species and genera.

Our variant analysis software identifies SNPs, indels and structural variants with high-accuracy using both DNA‑Seq and RNA‑Seq data. Combined with our uniquely accurate NUCLEAR fragment mapping software, it can perform variant discovery and genotyping simultaneously across thousands of individuals, reconstruct haplotypes for any ploidy model, and classify variants according to their sequence context.

Our complete solution for physical and optical mapping data includes a proprietary optical aligner and assembler, tools for assembling BAC sequencing data, and a visualisation/edition solution, allowing users to curate and improve on BioNano and physical maps and raw single-molecule data and to build complete chromosome pseudomolecule assemblies integrating physical mapping, optical and sequence data.