Sergey Koren

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.

This paper develops a long-read sequencing protocol to improve variant detection and genome assembly in a human genome, achieving high accuracy and contiguity.

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.

Genome in a Bottle benchmark of 12745 sequence-resolved insertions and deletions of 50 bp or more, integrating 19 calling methods, scores false negatives and false positives alike.

MetaMaps assigns long-read metagenomic sequences to species and estimates sample composition with high accuracy and scalability.

This paper presents the genome of the zebra mussel, Dreissena polymorpha, providing insights into its invasive success and creating a resource for invasive species research.

The paper presents a high-quality chromosome-scale reference genome for Anopheles funestus, significantly improving continuity and completeness compared to previous assemblies.

This paper presents a high-quality goldfish genome assembly and analyzes gene evolution after whole genome duplication, identifying gene divergence patterns across tissues.

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

The paper presents an improved Aedes aegypti genome assembly, AaegL5, which enhances biological understanding and vector control efforts by resolving key genomic features and identifying new targets for intervention.

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 examines how RefSeq database growth affects k-mer-based species classification accuracy, finding increased misclassifications and reduced species-level classifications over time.

The paper introduces a fast algorithm for computing whole-genome homology maps, achieving efficient alignment with high accuracy and coverage.

The paper introduces a fast approximate algorithm for mapping long reads to large reference databases, achieving high speed and precision by combining minimizers with MinHash identity estimation.

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.

The paper demonstrates de novo long-read genome assembly of Nippostrongylus brasiliensis using MinION data, revealing complex DNA repeats and haplotypic variants.

The paper presents an annotated genome assembly of the Aedes albopictus C6/36 cell line, revealing genetic features and gene expression patterns relevant to viral propagation.

MetaCompass improves metagenomic assembly by combining reference-guided and de novo methods, enhancing completeness and accuracy over existing approaches.

The paper uses nanopore sequencing to assemble a high-quality genome of Solanum pennellii, achieving high gene completeness and structural similarity to a reference genome.

The paper develops a scaffolding method using Hi-C data to improve long read genome assembly contiguity and demonstrates its accuracy on two organisms.

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.

This paper evaluates GRCh38 and de novo haploid assemblies, finding that GRCh38 remains superior for complex genomic regions and coding sequences despite improvements in newer assemblies.

The paper introduces a hybrid assembly method using long reads and short accurate reads to improve genome contiguity for a highly repetitive plant genome.

The paper compares the NK gene complex across mammals using new genome assemblies and annotations, revealing evolutionary patterns and balancing selection.

This paper presents a de novo mammalian genome assembly for the domestic goat using long-read sequencing, short-read validation, and chromatin interaction mapping, achieving high contiguity and resolving repetitive regions.

Mash estimates genome and metagenome distances using MinHash for efficient clustering and search of large sequence collections.

The paper introduces MHAP, a method using locality-sensitive hashing to improve genome assembly from single-molecule sequencing, achieving high-quality assemblies for multiple organisms.

The paper introduces Harvest, a suite of tools for rapid core-genome alignment and visualization of thousands of microbial genomes, showing high speed and accuracy.

The paper introduces iMetAMOS, an automated pipeline for ensemble genome assembly and validation, demonstrating its effectiveness on microbial genomes.