genome assembly

High quality chromosomal genome assemblies of three human Plasmodium species directly from natural infections

The paper generates high-quality chromosome-level genomes for three Plasmodium species from natural infections, improving understanding of their biology and evolution.

DIPLER: rapid k-mer-based locus identification

DIPLER identifies structurally complex loci using k-mer analysis and de novo assembly from low-coverage sequencing data.

Goat genome assemblies, nine breeds for pangenome contribution

The paper presents high-quality genome assemblies for nine goat breeds using long-read sequencing, contributing to pangenome construction and structural variant analysis.

High Quality, Long-Read Genome Assemblies of Two Virulent Field Isolates of Pyricularia oryzae from Portugal

Two Portuguese rice-blast fungus isolates were assembled from PacBio HiFi reads into near-complete genomes; one isolate lacks Avr-Pii, Avr-Pia and Avr-Pik yet remains virulent on two rice cultivars.

Genome-resolved ecology and evolution of the microbiome enabled by quantitative long-read metagenomics

This paper introduces LRQ, a long-read metagenomics method that enables absolute strain abundance measurement and resolves microbial evolution in a Crohn's disease patient over eight years.

Somatic haplotype reconstruction and variant recalibration from tumor-only long-read sequencing

LongPhase-TO reconstructs somatic haplotypes from tumor-only long-read sequencing, improving variant calling accuracy and haplotype block size.

Integrated optimization of experimental and computational workflows improves genome recovery in long-read gut metagenomics

Accurate MAG reconstruction from complex soil microbiome through combined short- and HiFi long-reads metagenomics

This study combines HiFi long-read and short-read sequencing to improve MAG recovery and binning accuracy in soil microbiomes.

Chromosome assembly for the Black bean aphid Aphis fabae

The paper presents two chromosome-scale assemblies of the Black bean aphid Aphis fabae using HiFi and Hi-C, revealing expanded UDP-glycosyltransferases linked to insecticide tolerance.

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.

Multidimensional variation and population stratification across 8000 complete human centromeres

Over 8,000 gapless human centromeres reveal population-stratified satellite-array, inversion and haplotype variation, multiple candidate kinetochore sites in 16.8% of centromeres, and single-base substitution rates comparable to flanking pericentromeres.

HPRC2: A human pangenome reference with near-complete coverage of common genetic variation

460 haplotypes from 230 genomes, selected to maximize common-variant coverage, capture 99.43% of All of Us common small variants and halve structurally unreliable regions and base errors versus HPRC1.

An active-matrix digital microfluidic platform for simultaneous short- and long-read viral genomic surveillance

This paper develops a digital microfluidic platform that enables simultaneous short- and long-read viral genomic surveillance with improved efficiency and accuracy.

TandemTwister: Scalable genotyping and advanced visualization of tandem repeats

TandemTwister is a tool for tandem repeat genotyping and visualization, showing high accuracy and speed across sequencing technologies and datasets.

A chromosome-scale, haplotype-resolved genome assembly of the barley stripe rust pathogen Puccinia striiformis f. sp. hordei

The paper presents a high-quality, haplotype-resolved genome assembly of the barley stripe rust pathogen Puccinia striiformis f. sp. hordei using long-read and Hi-C sequencing.

Long-read single-cell genomics: resolving chimeras in multiple displacement amplification

The paper develops lrSAGA, a tool to improve genome assembly from long-read MDA sequencing of single cells, achieving higher completeness and fewer misassemblies.

A global map for introgressed structural variation and selection in humans

Long-read phased assemblies from two Papuans plus 47 HPRC genomes map archaic introgressed structural variants, revealing 11 candidate archaic centromeres and 16 candidate adaptive SVs.

HyDRA: a pipeline for integrating long- and short-read RNAseq data for custom transcriptome assembly

HyDRA integrates long- and short-read RNAseq data to improve transcriptome assembly, identifying over 50,000 new long noncoding RNAs in ovarian and fallopian tube samples.

Draft genome assembly of the Woolly bottlebrush (Greyia radlkoferi) using Pacbio long-read sequencing technology.

This paper generates the first draft genome of Greyia radlkoferi using PacBio long-read sequencing, providing insights into its environmental resilience and medicinal properties.

GANGE: Achieving Sequencing Without Sequencing With Diffusion Guided Generative Genomic Transformer

GANGE is a deep-learning system that generates accurate genomic sequences from low-coverage, error-prone reads, reducing sequencing costs and enabling regulomics research without genome data.

High-resolution metagenome assembly for modern long reads with myloasm

Myloasm improves metagenome assembly using long reads, recovering more complete contigs and resolving antibiotic resistance genes.

Single-Platform Nanopore Sequencing Enables Diploid Telomere-to-Telomere Genome Assembly and Haplotype-Resolved 3D Chromatin Maps

This paper presents a Nanopore-only workflow for diploid T2T genome assembly and haplotype-resolved 3D chromatin maps, achieving high accuracy without hybrid polishing.

High-quality metagenome assembly from nanopore reads with nanoMDBG

nanoMDBG improves metagenome assembly from ONT reads, producing more high-quality MAGs with less computational resources than existing assemblers.

A chromosome-level assembly and functional genomic resources for the model annelid Capitella teleta

The paper presents a chromosome-level genome assembly and functional genomic resources for Capitella teleta, improving upon an outdated reference and enabling better analysis of multi-omic data.

NanoSimFormer: An end-to-end Transformer-based simulator for nanopore sequencing signal data

NanoSimFormer generates high-fidelity nanopore sequencing signals optimized for accurate basecalling, outperforming existing simulators across multiple datasets and tasks.

Convergent evolution of psilocybin biosynthesis by psychedelic mushrooms

Comparative mushroom genomics and fly-rearing experiments reveal an alternative psilocybin biosynthetic gene cluster in Inocybe corydalina, horizontal transfer of the canonical cluster, and incomplete defense against dipteran larvae.

Chromosome-scale genome assembly and linkage map for Silene uniflora reveal the recombination landscape in a rapidly evolving plant species

Chromosome-scale genome assembly of Malcolmia littorea using long-read sequencing and single-pollen genotyping technologies

This study presents a chromosome-scale genome assembly of Malcolmia littorea using long-read sequencing and single-pollen genotyping, revealing a genome twice the size of Arabidopsis thaliana.

MoGAAAP: A modular Snakemake workflow for automated genome assembly and annotation with quality assessment

MoGAAAP automates genome assembly and annotation using HiFi and other long-read data, producing quality assessments for comparative genomics.

Morphogenomic description of Cranifera cranifera (Chitwood, 1932) Kloss, 1960 from captive Blaptica dubia Serville, 1838 cockroach

Third nuclear genome for arthropod pinworms (Thelastomatoidea): a PacBio long-read Cranifera cranifera assembly (242 Mb, N50 43 kb, 90.5-94% BUSCO) plus a 24644-base mitogenome and male redescription.