Brian P. Walenz

The paper presents telomere-to-telomere genome assemblies of a Thoroughbred horse and donkey derived from a mule, revealing insights into equid centromere evolution and plasticity.

This study assembles human Robertsonian chromosomes, identifies a common breakpoint and centromere epigenetic changes, and explores structural features enabling their formation.

Verkko2 improves genome assembly by integrating proximity ligation data with long-read De Bruijn graphs, enabling complete telomere-to-telomere assemblies for diploid human genomes.

The paper presents the complete sequence of a human Y chromosome, correcting errors in the GRCh38 reference and adding over 30 million base pairs.

Verkko automates telomere-to-telomere diploid genome assembly using long-read sequencing and graph-based methods, achieving high accuracy in chromosome assembly.

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.

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

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.

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.

This study evaluates the impact of sequence depth and read length on long-read assembly quality for the maize genome, finding that lower depths and shorter reads result in fragmented assemblies.

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

The paper presents an updated horse reference genome, EquCab3, which improves contiguity and composition compared to the previous version, EquCab2.

Canu's tf-idf weighted MinHash overlapping and error-filtered sparse overlap graph yield complete Nanopore microbial genomes and contig NG50 above 21 Mbp for PacBio human and Drosophila.

The paper improves the Atlantic cod genome assembly using long-read sequencing and multiple assembly programs, revealing a high density of tandem repeats and heterozygous variation.