Arang Rhie

This paper introduces Winnowmap2, a long read mapping method that reduces allelic bias in repetitive sequences, improving variant calling accuracy in near-identical repeats.

The paper uses a complete human genome assembly to analyze epigenetic patterns in previously uncharacterized genomic regions, revealing methylation and chromatin accessibility features in satellite DNA and centromeres.

The paper improves a telomere-to-telomere human genome assembly by developing a repeat-aware polishing strategy, fixing 51% of errors and increasing assembly quality.

A gapless 3.055 billion bp human genome from HiFi and ultra-long nanopore reads resolves all centromeric arrays and acrocentric p-arms, adding 182 Mbp of new sequence.

The paper presents the first de novo repeat discovery and annotation of a complete human reference genome, identifying novel satellite arrays and characterizing new classes of complex repeats.

The paper presents a comprehensive analysis of fully assembled human centromeres, revealing their architecture, variation, and evolutionary dynamics at high resolution.

The T2T-CHM13 reference genome improves read mapping and variant calling across diverse samples, reducing false positives and enabling novel variant discovery.

Merfin improves variant filtering and polishing by using k-mer validation, enhancing precision and reducing errors in long-read assemblies.

The paper develops a pipeline for mitochondrial genome assembly and identifies errors and novel duplications in reference mitogenomes.

The paper summarizes methods and lessons from assembling 16 vertebrate genomes, highlights the importance of long-read sequencing, and introduces the Vertebrate Genomes Project to generate complete reference genomes for all vertebrate species.

FALCON-Phase uses long-read sequencing and Hi-C data to create phased diploid genome assemblies, achieving high accuracy in non-human species but lower accuracy in humans.

This paper completes the linear assembly of human chromosome 8, resolves long-standing gaps, and analyzes the evolutionary history of its centromeric regions across great apes.

The paper generates a high-quality reference genome for the vaquita and analyzes its demographic history, revealing long-term population stability and low genetic diversity.

Merqury estimates assembly consensus quality, k-mer completeness, and trio-based phasing from read k-mers alone, avoiding reference alignment; validated on Arabidopsis F1 hybrid and human NA12878 assemblies.

HiCanu improves genome assembly accuracy and haplotype resolution using HiFi long reads, achieving high contig size and consensus accuracy in human genomes.

The paper presents an improved genome assembly of Aedes albopictus, revealing new biological features and enabling population and developmental studies.

The paper presents a gapless, telomere-to-telomere assembly of the human X chromosome using ultra-long-read nanopore sequencing and complementary technologies.

The paper introduces a weighted minimizer sampling algorithm to improve long-read mapping accuracy, particularly in repetitive regions, by reducing false positives while maintaining match guarantees.

The paper introduces SALSA2, a Hi-C scaffolder that improves accuracy by using assembly graphs to correct inversion errors in chromosome-scale genome assemblies.

This study uses trio binning to assemble chromosome-length haplotigs for yak and cattle from an F1 hybrid, achieving high continuity and phasing accuracy.

The paper presents haplotype-resolved cattle genomes to identify structural variants and adaptation traits, finding expanded immune-related gene families and a fatty acid desaturase copy under positive selection in indicine cattle.

HLA*PRG:LA is a graph alignment model for HLA typing that achieves high accuracy across various sequencing data types.

This paper introduces trio binning, a method for assembling haplotypes from heterozygous genomes using parental short reads, achieving high accuracy in diploid reconstruction.

Nanopore-only sequencing of GM12878 across 39 MinION flowcells (91.2 Gb) yielded an assembly with NG50 ∼3 Mb; adding 5× ultra-long reads raised NG50 to 6.4 Mbp.