variant calling

Optimizing genome assembly, chromosome synteny, and genetic variant discovery from Oxford Nanopore sequences of Dermacentor reticulatus ticks

The paper optimizes genome assembly and variant discovery for Dermacentor reticulatus ticks using Oxford Nanopore sequencing, identifying workflow parameters that yield high-quality assemblies and genetic insights.

Population-based Characterization of PTEN Hamartoma Tumor Syndrome

The paper identifies 55 individuals with pathogenic PTEN variants in a population-based cohort, revealing higher prevalence and broader clinical features of PHTS than previously recognized.

The genomic complexity of invasion: cryptic lineages, founder effects, and polygenic sex determination in armored catfish

The paper evaluates biocontrol feasibility in invasive armored catfish by analyzing genomic diversity, population structure, and sex determination mechanisms.

Byte-exact, format-aware compression for FASTA, FASTQ, BED and VCF files

NYX provides fast, lossless compression for common omics data formats, achieving better compression ratios and speed than existing codecs.

MAJEC: unified gene, isoform, and locus-level transposable element quantification from RNA-seq

MAJEC improves TE quantification by jointly estimating gene, isoform, and locus-level TE counts from RNA-seq, reducing exon-overlap contamination and increasing accuracy.

The role of methylation and structural variants in shaping the recombination landscape of barley

This study identifies genomic features that explain recombination variation in barley, showing methylation and structural variants jointly determine recombination hotspots and coldspots.

Historical plant embryos as alternative sources of ancient DNA for whole genome sequencing

The paper isolates DNA from seed embryos of historical plant specimens to improve ancient DNA quality for whole genome sequencing, finding embryos provide better DNA preservation than leaves in some species.

vartracker: an end-to-end tool for pathogen longitudinal variant analysis and visualisation

vartracker analyzes and visualizes pathogen variants over time, tracking their evolution and classification across longitudinal datasets.

Genomic Characterization of 30 Lytic Klebsiella pneumoniae Bacteriophages

This study characterizes 30 lytic Klebsiella pneumoniae bacteriophages, finding diverse genomic structures and no virulence or antibiotic resistance genes, with potential as antimicrobial agents against carbapenem-resistant K. pneumoniae.

Complete timing of copy-number amplification histories reveals whole-genome duplication dynamics and coincident oncogene amplification bursts

The paper introduces a method to time copy-number amplification events in cancer genomes, revealing that whole-genome duplication (WGD) enables bursts of oncogene amplification.

Whole-genome characterization of Plasmodium falciparum population structure and drug resistance across Uganda and neighboring countries

The paper characterizes the population structure and drug resistance of Plasmodium falciparum in Uganda and neighboring countries using whole-genome data, identifying key resistance-associated haplotypes.

A reference genome without a virus: cDNA reconstruction reveals the provenance and function of the MS2 phage sequence

The paper reconstructs the MS2 phage genome using cDNA and shows that the current NCBI reference genome does not produce infectious phage, highlighting the need to verify reference genome infectivity.

Rapid and Specific Identification of Emerging Trichophyton mentagrophytes Genotype VII Using an In-House Developed and Validated Real-Time PCR Assay

This paper develops a real-time PCR assay for rapid and specific identification of Trichophyton mentagrophytes genotype VII with high sensitivity and specificity.

Integrated Clinical-Genomic Reanalysis Identifies Diagnostic Gaps and Candidate Genes in a Pediatric Rare Disease Cohort

A KIAA0586 c.1815G>A Founder Allele Associated with Short-Rib Polydactyly Syndrome Type IV in Romani Families

The paper identifies a KIAA0586 c.1815G>A founder allele associated with short-rib polydactyly syndrome type IV in Romani families and reports its higher frequency in Hungarian Romani individuals.

Gene flux shapes diversity and evolution of the ancient 17q21.31 inversion polymorphism

The paper measures recombination rates between inversion haplotypes at 17q21.31, finds gene flux occurs despite suppression, and shows its impact on fertility and genetic diversity.

Genomic structural variation in clownfish adaptive radiation

This study characterizes structural variation across 16 clownfish species, identifying extensive SVs and clarifying inversion events on chromosomes 18 and 9.

Mutation spectra across 3,034 Saccharomyces cerevisiae genomes distinguish the Georgian Wine population

The paper analyzes mutation spectra across 3,034 Saccharomyces cerevisiae genomes to show increased variation in wine-associated populations, particularly in Georgian Wine strains.

Analysis of SpCas9 on- and off-target effects in high efficiency multiplex editing in Arabidopsis

The paper analyzes SpCas9 on- and off-target effects in Arabidopsis using high-efficiency multiplex editing and finds high specificity but potential for extensive on-target modifications at complex loci.

Identifying, phasing, and structurally annotating sex chromosomes for genome assemblies using CBS-tools

CBS-tools identifies, phases, and annotates sex chromosomes using k-mer analysis from whole-genome sequencing data across multiple species.

Genome assembly of the C4 grass Themeda triandra confirms karyotype orthology with sorghum and reveals genetic variation across diverse environments

The paper assembles the genome of Themeda triandra, finds syntenic relationships with sorghum, and identifies genetic variation linked to environmental adaptation.

Confirmation of gamma irradiation mediated inactivation of a Vero adapted African swine fever virus Lisbon 60 strain for molecular assays

This study confirms that gamma irradiation at 50 kGy fully inactivates ASFV while preserving nucleic acid integrity for molecular assays.

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.

HipHap: Haplotype Assignment and Confidence Scoring for Diploid Reference Genomes

HipHap improves haplotype assignment and confidence scoring for diploid genomes by aligning reads to each haplotype separately and introducing a quality score.

Nailpolish: Reference-free UMI deduplication and consensus read generation

Nailpolish reduces error rates and improves deduplication of UMI-tagged long reads across multiple sequencing technologies and protocols.

MaveMD: A functional data resource for genomic medicine

MaveMD provides a clinical interface for MAVE data to classify variants of uncertain significance and improve genetic medicine outcomes.

SCAR: Controlled mutations, ancient DNA damage, and fragmentation of fasta and fastq sequences

SCAR introduces controlled mutations, fragmentation, and damage to sequencing data for benchmarking analyses affected by these factors.

Plasmid architecture determines the stability of inverted terminal repeats in adeno-associated virus vectors

The paper identifies position-dependent ITR instability in AAV plasmids and develops a stable rAAV vector with full-length native ITRs.

DNA:RNA hybrid mutational landscapes reveal a common route to geneticinstability in evolving genomes

The paper identifies mutational signatures caused by DNA:RNA hybrids in yeast genomes, revealing a common mechanism of genetic instability through repair pathways.

Perfect 21-nucleotide matches to beneficial fungi are common in canonical antifungal dsRNA targets: an in-silico off-target hazard screen for spray-induced gene silencing

The paper screens dsRNA constructs for off-target effects on beneficial fungi and finds many have perfect 21-nt matches, highlighting a regulatory gap.