genome assembly

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.

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.

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.

High-efficiency, transgene-free plant genome editing by viral delivery of an engineered TnpB

Tobacco rattle virus delivery of engineered ISDra2 variant eTnpBc and its guide RNA as a single transcript achieves up to 90% somatic and 100% heritable editing in Nicotiana benthamiana.

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.

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.

Oatk: a de novo assembly tool for complex plant organelle genomes

Oatk combines a sparse syncmer assembler, profile HMM gene databases and graph path search to assemble plastomes and mitogenomes from HiFi reads for 195 plant species.

Complex genetic variation in nearly complete human genomes

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.

Phylogenomics and metabolic engineering reveal a conserved gene cluster in Solanaceae plants for withanolide biosynthesis

Comparing nine Solanaceae genomes reveals a conserved withanolide gene cluster; three of its P450s, expressed in yeast and N. benthamiana, oxidise 24-methyldesmosterol toward the withanoside V aglycone.

Hybridogenetic reproduction of Pelophylax water frogs from different R-E hemiclonal population systems from Eastern Ukraine: selective mortality, clonal and ploidy diversity

Siverskyi Donets water frog systems lacking P. lessonae split into diploid-only and diploid-plus-triploid hybrid types, with clonal, low-diversity L-genomes and steep tadpole-to-adult loss of P. ridibundus.

On the path to reference genomes for all biodiversity: lessons learned and laboratory protocols created in the Sanger Tree of Life core laboratory over the first 2000 species

Across 4883 species, standardised high-molecular-weight DNA extraction passed 96% of chordate and 91% of plant species, while fungi failed at 34.2%; ultra-low-input PacBio libraries rescue many low-yield samples.

Synchronized long-read genome, methylome, epigenome, and transcriptome for resolving a Mendelian condition

Pooling Fiber-seq gDNA with concatenated MAS-Seq cDNA in one PacBio run gives phased genome, methylome, chromatin, and transcriptome, exposing four gene disruptions from one X;13 translocation.

Logan: Planetary-Scale Genome Assembly Surveys Life's Diversity

Assembling the Sequence Read Archive (27.3 million accessions) with over 100-fold compression enables minutes-scale k-mer search and mining of enzymes, plasmids, proteins and viral reactivation.

How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies

Roughly 25× short-read depth polishes nearly all residual errors in Nanopore-only bacterial assemblies; new '--careful' modes in Pypolca and Polypolish largely avoid introducing low-depth errors.

The variation and evolution of complete human centromeres

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.

Rapid and sensitive detection of genome contamination at scale with FCS-GX

FCS-GX, a hashed k-mer cross-species aligner with a 709 Gbp curated database, screens most genomes in 0.1-10 minutes and flagged 36.8 Gbp of contamination in GenBank.

Hagfish genome illuminates vertebrate whole genome duplications and their evolutionary consequences

Chromosome-scale inshore hagfish genome places 1R before the cyclostome-gnathostome split and 2R in the gnathostome stem, and reveals two cyclostome-specific duplications (CR1, CR2).

An efficient error correction and accurate assembly tool for noisy long reads

NextDenovo corrects noisy Nanopore reads faster and more accurately than Canu and Necat; its maize and 35 human-genome assemblies are more contiguous, with fewer misassemblies, than Flye's.

YaHS: yet another Hi-C scaffolding tool

YaHS, a C command-line Hi-C scaffolder, normalises inter-contig contacts by intra-contig medians, yielding more contiguous, accurate chromosome-scale scaffolds than SALSA2 and pin_hic.

Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs

Gfastats, a C++ tool, computes genome assembly statistics in linear time, converts between FASTA, FASTQ and GFA files, and edits assemblies through a bidirected graph.

The complete sequence of a human genome

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.

Blueprint for Phasing and Assembling the Genomes of Heterozygous Polyploids: Application to the Octoploid Genome of Strawberry

Trio-binned PacBio HiFi reads plus a 3.6 M-variant recombination map give phase-resolved assemblies of octoploid strawberry 'Royal Royce' and FaRR1, a 786.5 Mb haploid reference with 28 pseudomolecules.

Significantly improving the quality of genome assemblies through curation

gEVAL-assisted manual curation of 111 VGP and DToL assemblies averaged 221 interventions per Gb, raising mean scaffold N50 by 40% and cutting scaffold counts by 29%.

Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies

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.

CheckV: assessing the quality of metagenome-assembled viral genomes

CheckV estimates completeness of metagenome-assembled viral contigs against GenBank plus 76,262 metagenome-derived complete genomes and trims host flanks; 86.9% of IMG/VR contigs were low-quality.

BlobToolKit Interactive quality assessment of genome assemblies

BlobToolKit combines GC proportion, read coverage and taxonomic hits per contig in an interactive browser Viewer, exposing contaminants and cobionts across public eukaryotic genome assemblies.

Sequence and annotation of 42 cannabis genomes reveals extensive copy number variation in cannabinoid synthesis and pathogen resistance genes

Long-read assemblies of an inbred cannabis trio plus whole-genome sequencing of 40 cultivars link cannabinoid synthase gene deletions to chemotype and associate CsTLP1 loss with powdery mildew susceptibility.

HyPo: Super Fast & Accurate Polisher for Long Read Genome Assemblies

Hybrid polisher that leaves solid-k-mer-supported contig regions untouched gave HG002 long-read assemblies fewer errors than Racon in under one-third the time and about half the memory.