genome assembly

Cell-in-drop genotyping detects megabase-scale loss of heterozygosity as a quantitative marker for CRISPR-Cas9 on-target toxicity

Genomic forecasting links climate-associated variation to spring phenology in the European wild apple, a crop wild relative of the cultivated apple

The paper tests if climate-associated genomic variation predicts phenotypic adaptation in European wild apple, finding genomic offsets link to bud-break timing but not other traits.

A genomic baseline for long-term monitoring of economically important aquatic species in the Netherlands

The paper establishes a genomic baseline for six aquatic species in the Netherlands using SNP data to assess population structure, diversity, and conservation priorities.

Genome assemblies and annotations of the poneroid ants Platythyrea mocquerysi (Ponerinae) and Stigmatomma oregonense (Amblyoponinae)

The paper presents draft genome assemblies for two ant species, analyzing genome size variation and gene family expansions related to brood management strategies.

RASTRO: Branching Point Decision-Making in Unitig Graphs

RASTRO improves unitig graph path selection by using sequence-based models to identify read-supported branching points in HIV-1 and SARS-CoV-2 assemblies.

Sum-h2, enabling genetic discovery for deep learning-derived phenotypes through a fast evaluation framework and arena of performance

The paper introduces sum-h2, a fast framework for evaluating genetic discovery from deep learning-derived phenotypes using heritability measures, and establishes a Genetic Discovery Arena for benchmarking.

PfPHAST: Plasmodium falciparum Public Health Amplicon Sequencing Tool, a Streamlined Panel for Malaria Genomic Surveillance

PfPHAST is a streamlined amplicon sequencing panel for malaria genomic surveillance, offering better quality control and cost efficiency than MAD4HatTeR without sacrificing performance on shared targets.

Sparse Linear Algebra Accelerates Genotype Representation Graph Computation at Biobank Scale

This paper introduces Mikado, a method using sparse linear algebra to accelerate genotype representation graph computations, significantly improving speed over existing tools on large biobank datasets.

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

Genome report: Genome sequence of Phymata mystica (Evans), an ambush bug

The paper reports the genome sequence of Phymata mystica, an ambush bug, and identifies conserved venom proteins, providing insights into venom evolution in Heteroptera.

FORGEPHAST: A fast, haplotype-first complex population and phenotype simulator for biobank-scale simulation

FORGEPHAST simulates large synthetic cohorts with controlled genetic and phenotypic properties, showing polygenic risk score performance varies by phenotype architecture, ancestry, and variant coverage.

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.

PlasChain: an algorithm for improving long plasmid reconstruction from metagenome assemblies

PlasChain improves long plasmid reconstruction from metagenome assemblies by addressing fragmentation and false positives, outperforming existing methods in recovering long plasmids.

Assessing the Role of Marker Density and Minor Allele Frequency on Machine Learning Driven Genomic Selection Accuracy in Grapevine

This study evaluates how marker density and minor allele frequency affect genomic selection accuracy in grapevine using machine learning models and conventional methods.

Compound Delivery of eVLPs Enhances Prime Editing for Targeted Genome Engineering and High-Throughput Screening

This paper introduces PRIME-VLP, a delivery strategy that enhances prime editing efficiency for genome engineering and high-throughput screening using eVLPs.

Complex genetic architecture underlying the plasticity of tobacco leaf width provides insight into across-environment genomic prediction

This study identifies QTLs associated with leaf width and its plasticity in tobacco and develops a GEAI model for cross-environment prediction, improving accuracy by 8.7%.

SELECT-seq allows Pre-Sequencing Enrichment of SNP Edits in One-Pot Single-Cell Whole-Transcriptome Sequencing

SELECT-seq enables rapid, scalable SNP-specific enrichment of single cells for genotype-phenotype analysis without cloning.

Enhancing predictive accuracy of yield traits in cassava through multi-trait genomic prediction

This study compares single-trait and multi-trait genomic prediction models for cassava yield traits, showing that multi-trait models improve predictive accuracy and reduce phenotyping burden.

CYClones: A highly powered, fully genotyped, 8-parent yeast mapping population

CYClones is a yeast mapping population with high genetic diversity and power to detect low-heritability variants, enabling genetic dissection of complex traits.

Towards genetic indicators in ectomycorrhizal fungi: estimating the effective population size

The paper estimates effective population size (Ne) in ectomycorrhizal fungi using genetic data and finds biases in Ne estimation due to clonality and population structure.

Dissecting genetic variance structure and evaluating genomic prediction models for single-cross hybrids derived from Stiff Stalk and Non-Stiff Stalk maize heterotic groups

This study evaluates genomic prediction models for maize hybrids using GBLUP-based multi-kernel models to estimate genetic variance components and predict hybrid performance.

Genomic insights into bacterial kidney disease resistance in Arctic charr (Salvelinus alpinus) via a 72k SNP array

This study develops a 72k SNP array to assess BKD resistance in Arctic charr and finds genomic prediction is feasible with moderate accuracy.

Identification of heterotic group-specific haplotypes and impact of residual inbreeding on grain yield of maize elite hybrids

This study identifies heterotic group-specific haplotypes and shows that residual inbreeding from commercial hybrids negatively impacts maize grain yield.

The first reference genome assembly of the Chilean sea fig (Carpobrotus chilensis)

The paper presents a draft genome assembly of Carpobrotus chilensis, revealing low heterozygosity, high transposable element content, and low sequence divergence from its invasive relative C. edulis.

From Nuisance to Signal: Leveraging Close Relatives in Biobank-Scale Demographic Inference

This paper evaluates the impact of retaining close relatives on demographic inference using IBD-based methods and finds that retaining relatives reduces bias in Ne estimates.

GnnDebugger: GNN based error correction in De Bruijn Graphs

GnnDebugger uses Graph Neural Networks to correct errors in De Bruijn Graphs, improving genome assembly accuracy for diploid genomes with low coverage.

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.

Tumour evolution as ground truth for cancer whole-genome sequencing

This paper introduces SCOUT, a synthetic whole-genome sequencing resource for benchmarking cancer genomic analysis, revealing performance issues in complex tumours and highlighting the importance of evolutionary ground truth.

BINSEQ: A Family of High-Performance Binary Formats for Nucleotide Sequences

BINSEQ introduces binary formats for sequencing data to enable faster parallel processing, reducing analysis time for genome and transcriptome studies.

Pharmacological stress exposes hidden allelic background effects in genetic interaction screen normalisation

The paper shows that pharmacological stress reveals hidden allelic background effects in genetic interaction screens, using fission yeast and Torin1 to demonstrate divergent fitness profiles.