ImpuT2T: Pangenome-Based Patching for Human Genome Assemblies
Lin, M.-J.; Shivakumar, V. S.; Langmead, B.; Human Pangenome Reference Consortium,
Show abstract
With improvements in sequencing and assembly have come many high-quality telomere-to-telomere assemblies and reference pangenomes. However, the long-read sequencing recipes needed for high quality assemblies are expensive, and out of reach for many research groups. Here we propose ImpuT2T, a method that takes an assembly produced via inexpensive HiFi sequencing reads, and uses a panel of T2T (or near-T2T) assemblies to scaffold and fill ("patch") the gaps between the HiFi contigs. Benchmarking against reference assemblies demonstrates that ImpuT2T is highly effective at patching human HiFi assemblies, consistently outperforming existing patching approaches. Moreover, we show that including more haplotypes in the pangenome improves the quality of the patched assemblies, with the greatest gains achieved using the full HPRC Release 2 pangenome.
Matching journals
The top 2 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Highly accurate assembly polishing with DeepPolisher 96%
- An Algorithm for Sequence Location Approximation using Nuclear Families (ASLAN) Validates Regions of the Telomere-to-Telomere Assembly and Identifies New Hotspots for Genetic Diversity 96%
- Gaps and complex structurally variant loci in phased genome assemblies 96%
Similar papers in this journal
Similar papers in this journal
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.