Gunjan Baid

The paper introduces Minigraph-Cactus, a pangenome pipeline that constructs pangenome graphs directly from whole-genome alignments, demonstrating improved performance in mapping and variant calling across human and Drosophila data.

The paper presents a draft human pangenome reference that improves variant discovery and structural variant detection compared to existing references.

The paper shows recombination between heterologous human acrocentric chromosomes using pangenome data, revealing pseudo-homologous regions linked to Robertsonian translocations.

The paper evaluates variant calling in difficult genomic regions using short- and long-read sequencing, showing improved performance with new methods and multi-technology approaches.

The paper introduces a haplotype-aware variant calling pipeline for nanopore and PacBio HiFi data, achieving high accuracy in variant detection and de novo assembly polishing.

DeepConsensus improves PacBio HiFi read accuracy and assembly quality using a gap-aware transformer model.

DeepTrio improves variant calling in family trios using deep learning, achieving higher accuracy than DeepVariant, especially at lower coverages.

The paper provides a dataset of 9 gold-standard samples sequenced on multiple platforms and protocols to benchmark sequencing and analysis methods.