Mikko Rautiainen

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.

Hybrid HiFi/ultra-long ONT assemblies of 65 diverse humans yield 130 haplotypes, 1,246 complete centromeres, and a pangenome panel enabling short-read genome inference at median QV 45.

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.

This paper demonstrates that ONT Duplex sequencing combined with Pore-C data can assemble complete, high-quality human and plant chromosomes with base accuracy over 99.999%.

A second complete human centromere set (CHM1) plus 31 nonhuman primate centromeres reveals extensive α-satellite higher-order repeat variation, kinetochore repositioning, and saltatory emergence of new repeats.

Ribotin assembles full-length rDNA morphs using long reads to address assembly challenges in repetitive regions.

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

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.

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.

MBG constructs sparse de Bruijn graphs from HiFi reads, outperforming existing tools and efficiently assembling genomes.

GraphAligner aligns long reads to genome graphs efficiently and accurately, outperforming existing tools in speed and memory usage.

The paper develops a diploid assembly-based benchmark for variants in the MHC region using HG002 data, identifying 21496 small variants with high concordance to clinical HLA types.

This paper introduces a novel two-stage method for polyploid haplotype phasing using long reads, achieving lower error rates than existing methods in challenging regions.

AERON quantifies transcript expression and detects gene-fusions from long RNA reads, showing accuracy on simulated and real data.

This paper generalizes sequence-to-sequence alignment algorithms to graphs, achieving significant speedups for aligning sequencing reads to variation graphs.

The paper introduces an algorithm to align sequences to node-labeled directed graphs in O(V + mE) time, improving efficiency for genome assembly and variant calling.