Shloka Negi

A complete diploid human genome benchmark for personalized genomics

T2T-HG002v1.1, a complete diploid HG002 assembly lacking detectable errors over 99.4% of its length, enables genome-based benchmarking of assemblies, sequencing reads, and phased variant calls.

Structural variant discovery and diagnostic impact in rare diseases from short-read and long-read sequencing

This study evaluates the diagnostic yield of short-read and long-read sequencing in rare diseases, finding limited added value from long-read sequencing despite increased variant discovery.

Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe

The paper updates Giraffe to map both long and short reads to large pangenome graphs, showing improved speed and accuracy compared to existing tools.

Long-read sequencing resolves the clinically relevant CYP21A2 locus, supporting a new clinical test for Congenital Adrenal Hyperplasia

This paper uses long-read sequencing to comprehensively identify pathogenic variants in the CYP21A2 locus for Congenital Adrenal Hyperplasia, including phasing and module counts, improving diagnostic accuracy.

Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection

This study evaluates the diagnostic yield of long-read nanopore sequencing in rare disease detection, finding it covers more genes and detects additional variants compared to short-read sequencing.

Haplotype-Resolved Long-Read Sequencing in Hundreds of Diverse Brains Identifies Structural Variant Impacts on Expression and Allele-Specific Methylation

The paper uses long-read sequencing to identify structural variants and their impacts on gene expression and methylation in diverse human brain samples.