genome assembly

HiFi-Helper: A reproducible workflow for genome assembly from HiFi reads alone

HiFi-Helper provides a workflow for genome assembly using HiFi reads, achieving quality comparable to older methods with less time and resources.

Application of the CPER reverse genetics system for genetic engineering of rabies virus

This paper develops a CPER-based reverse genetics system for rabies virus, enabling the generation of recombinant viruses with various genetic modifications.

Towards On-Site Paleogenomics: Application and Perspective of Nanopore Sequencing with Ancient DNA

This study applies nanopore sequencing to ancient DNA from the Early Jomon period, demonstrating its ability to generate genome-wide data and enable rapid, on-site paleogenomic analysis.

Genetic population structure and demographic history of Pacific cod in Japanese waters: Implications for stock identification using SNP markers

This study identifies three genetic groups in Pacific cod in Japanese waters using SNPs and shows that outlier SNPs improve stock identification accuracy.

The complete genome of the KOLF2.1J reference iPSC line

The paper generates and characterizes a custom genome assembly for the KOLF2.1J iPSC line to improve genomic analysis accuracy compared to standard references.

A robust and high-efficiency Rhizobium rhizogenes hairy root transformation platform for Vaccinium

This paper develops a high-efficiency Rhizobium rhizogenes hairy root transformation system for Vaccinium, achieving up to 80% transformation efficiency and enabling gene validation and genome editing.

Sex chromosome identification and genome curation, at scale, from a single individual with SCINKD

This paper introduces SCINKD, a tool to identify sex chromosome linkage groups and curate misassembled regions in a single diploid genome.

Complete sequencing of the mouse pseudoautosomal region, the most rapidly evolving 'chromosome'

The paper sequences the mouse pseudoautosomal region, revealing its structure and evolutionary dynamics.

diempy: fast and reference-free genome polarisation

diempy provides a fast, reference-free method for genome polarisation, enabling analysis of population structure and admixture without pure reference panels.

Automatic Generation of Model Sequences for Complex Regions in Assembly Graphs

The paper introduces TTT, an algorithm that resolves assembly graph tangles in genomes, improving the accuracy of complex regions in reference assemblies.

CollapsedChrom: resolving the assembly of collapsed chromosomal segments in polyploid genomes of the model grass genus Brachypodium

The paper develops a method to resolve collapsed chromosomal segments in polyploid Brachypodium genomes, improving assembly quality and capturing genomic architecture.

A chromosome-level genome assembly of the South African indigenous, Kolbroek pig, Sus scrofa domesticus

This paper presents a high-quality chromosome-level genome assembly of the Kolbroek pig, providing a genetic resource for studying genetic variation and improving breeding programs.

A near gap-free haplotype-resolved genome assembly of Zoysia japonica uncovers intra-subgenomic gene expression and regulatory variation

The paper presents a high-quality haplotype-resolved genome assembly of Zoysia japonica and identifies gene expression and regulatory variation between haplotypes.

Chromosome-level genome assembly and annotation of the parthenogenetic nematode Acrobeloides nanus

This paper presents a chromosome-level genome assembly of Acrobeloides nanus, revealing genomic features and adaptations related to parthenogenesis and desiccation resistance.

Diversity and Genomic Organization of Non-B DNA Motifs in Haplotype-Resolved Human Genome Assemblies

The paper analyzes non-B DNA motifs in haplotype-resolved human genomes, revealing population-level variation and structural stability patterns in repetitive genomic regions.

The complete chloroplast genome of Garcinia binucao (Blanco) Choisy, an indigenous fruit from the Philippines

This study reports the first complete chloroplast genome of Garcinia binucao, providing genomic resources for conservation and genetic research.

Telomere-to-telomere assembly and haplotype analysis of tetraploid Dendrobium officinale illuminate Orchidaceae polyploid evolution and mycorrhizal symbiosis genes

This paper presents the first telomere-to-telomere genome assembly of Dendrobium officinale, identifies tetra-allelic genes, and explores SWEET gene family evolution and mycorrhizal functions.

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 genome assembly of a vernal pool specialist amphibian, the Western Spadefoot, Spea hammondii

The paper presents a chromosome-level genome assembly for the Western Spadefoot, Spea hammondii, using long-read and proximity ligation data, enabling population genomic studies for conservation.

Transposable Element Diversification and the Evolution of Peltigerales Lichen Symbionts

This study uses long-read metagenomic sequencing to analyze Peltigerales lichen symbionts, revealing high transposable element content and their potential role in lichenization evolution.

A chromosome-scale genome assembly for Clark's Nutcracker (Nucifraga columbiana)

The paper presents a chromosome-scale genome assembly for Clark's Nutcracker and reports on population genetic findings.

Too rare to be random: genetic finding suggests previously unrecognized path of mutagenesis

The paper identifies a new genotypic configuration in twins with neurodevelopmental disorder, suggesting a previously unrecognized mutagenesis pathway.

The FORGENIUS genomic resources: new genotyping tools and genomic data for 23 forest tree species and their Genetic Conservation Units

A haplotype-phased male genome sequence of the stinging nettle, Urtica dioica ssp. dioica

The paper presents a haplotype-resolved genome sequence of a male stinging nettle, confirming structural variation and features associated with sex determination.

FAMeDB: A curated Database for the analysis of Fungal Aromatic Compound Metabolism

FAMeDB is a curated database of fungal proteins involved in aromatic compound metabolism, providing tools for omics analysis and genomic comparisons across 65 fungal species.

Genetic Surveillance Reveals Differential Evolutionary Dynamic of Anopheles gambiae Under Contrasting Insecticidal Tools used in Malaria control

This study uses genomic data to analyze evolutionary dynamics of Anopheles gambiae under different insecticidal tools, revealing distinct resistance mechanisms and allele frequency shifts.

Genetic correlation analysis identifies TMEM106B, ACE, and ERC2 as genetic loci shared between Alzheimer's disease and primary psychiatric disorders

Fully Phased Telomere-to-Telomere Assemblies for Thoroughbred Horse and Donkey Haplotypes derived from a Mule Illuminate the Peculiar Evolution of Equid Centromeres

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.

Calcium signals natural transformation in Acinetobacter baumannii

This paper identifies calcium as a key inducer of natural transformation in Acinetobacter baumannii, revealing both transcriptional and structural mechanisms by which calcium activates type IV pilus function.

Genomic diversity, population structure and admixture in native cattle breeds of Benin

This study analyzes genetic diversity and admixture in Benin's cattle breeds, finding significant differentiation between taurine and zebu breeds and gene flow from zebu to taurine due to adaptive factors.