All-to-all linear mapping of multiple denovo assemblies enables intra-species gene content variation exploration

A high-quality reference genome is a great starting point, yet in many plant species the genomic diversity within the species can be as high as 50% of the genomic sequence. The discovery of genomic variations is a hot scientific subject in many research papers, but current alignment (“re-seq”) or transcript based comparisons reveal only partial and incomplete results. Only NRGene’s full genome-to-genome approach allows the full discovery of genomic variations and structural variations such as translocations, PAVs, and CNVs.

Outstanding results

Who can benefit

Get the full genomic picture of your species based on a comparative analysis of multiple varieties


Multiple genomes constructed to pseudo-chromosomes


Use the full genome-to-genome maps for robust exploration of genomic variation


Don’t lose information! Extensive gene variation analysis including Presence / Absence, Copy Number and Structural Variants (PAV CNV and SV)

How it works

Mapping and comparing several whole genomes to capture the full and true diversity within the species.
First, an all-to-all mapping of all the genomes is performed, generating multiple text files that include the mapping of each individual genome to every other genome. Further, transcriptomic data is mapped to each of the genomes. Combining the genomes and the transcriptome mapping, a pair-wise comparison of the genic content of the genomes is conducted resulting in detection of SV (structural variations, e.g. translocations), PAVs (Presence/Absence Variation) and CNVs (Copy Number Variations).

NRGene has incorporated multiple assemblies to enable us to describe more diversity in our lines than could be detected by previous methods. They’ve really accelerated our research."


of Munich University, Germany.

Frequently Asked Questions

Which organisms are supported for this service?

Any organism for which there are homozygous diploid de novo assemblies of up to 5Gb. Allopolyploids genomes may be included (e.g. cotton, sunflower, pepper, tomato, brassica, cucurbits and many more)

How can I visualize the results?

NRGene has developed a customized version of the IGV browser (Broad Institute) which was made available in January 2019. All PanMAGIC delivery files can be visualized using this browser which can be downloaded upon registration at

What is PanMAGIC good for?
PanMAGIC provides you with a base-pair resolution comparison of two varieties with an unbiased placement of sequence data via GenoMAGICTM. PanMAGIC provides a unique analysis of gene copy number, presence/absence and structural variaions (e.g. translocation).