New visualisation of genomic variants in the context of genomic alignments 

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We have developed a novel visualisation to enable the investigation of structural variants (SVs) in the context of functional elements, pairwise alignments and segmental duplications. Developed in collaboration with the Human Genomic Structural Variation Consortium (HGSVC), with genomic alignment data provided by the Human Pangenome Reference Consortium (HPRC), the new Alignments viewer makes it easier to explore haplotype-specific variation.

Long read sequencing technologies now enable the assembly of complete haplotype sequences and the resolution of complex genetic variation. The NIH- funded HGSVC exists to characterise and improve understanding of the full spectrum of human genomic variation. As members of the consortium, we have created this novel interactive visualisation which is available on the new Ensembl website.

The Alignments viewer makes use of genomic alignment data generated by the NHGRI-funded Human Pangenome Reference Consortium as part of the HPRC Data Release 2.

You can navigate to the Alignments viewer from the icon on the new Ensembl homepage (https://beta.ensembl.org/).

From here, you can pick a reference assembly, a region and a haplotype assembly to view.

The Alignments Viewer has the following components –

  • Genomic alignment – shows the alignment between a pair of reference and haplotype assemblies.
  • Haplotype variants track-  displays variants called against the reference for alternative haplotype assembly. 
  • Gene tracks – this track is available for both reference and alternative assemblies respectively above and below the alignment.
  • Segmental duplication track – available for both reference and alternative assemblies respectively above and below the alignment, where data is available.
  • HGSVC3 variant track – shows all the variants called in the HGSVC phase 3 analysis for this reference assembly.
  • dbSNP short variants track – shown for the reference assembly.

There are currently six haplotypes available for investigation and more will be added in the near future. The application supports joint or individual assembly scrolling, has configurable track selection and the option to search by gene symbol. See the full documentation for more information. 

The Alignments viewer facilitates visualisation of the complete catalogue of genomic variation observed within a haplotype in a single view and will enable easier investigation and understanding of more complex regions. As always, we welcome your feedback as we continue to improve Ensembl’s tools for genomic analysis.

Authors: Sarah Hunt and Thomas Walsh