variant calling

The biochemical composition of coronavirus Nucleocapsid proteins drives the bicistronic properties of their sub-genomic mRNAs

The paper identifies conserved overlapping accessory ORFs in coronavirus N genes and shows that nucleotide and codon biases drive their formation.

Residual barcode-like sequences and barcode-associated artifacts after Dorado and Barbell preprocessing of metagenomic reads

The paper evaluates Dorado and Barbell preprocessing tools for metagenomic reads, finding Barbell reduces barcode-like sequences more effectively while retaining most reads.

Hybrid RY-mers increase aDNA alignment sensitivity

This paper introduces hybrid RY-mers to improve aDNA alignment sensitivity and efficiency, showing higher accuracy and reduced runtime compared to existing methods.

Somatic Structural Variant Discovery from Tumor Specific Strings Computed Against a Draft Composite Germline Reference

VESPA-SS detects somatic structural variants from long-read sequencing data without requiring read mapping or a high-quality germline reference, achieving high F1 scores on cancer cell lines.

Structural Variant Aware Identity-by-Descent Detection on Pangenome Graphs

GIBD detects IBD segments in pangenome graphs and annotates them with structural variants, outperforming existing methods in accuracy and speed.

Somatic structural variation discovery on cancer pangenome graphs

JANUS discovers somatic structural variants in cancer genomes using a pangenome graph approach, achieving high accuracy and efficiency compared to traditional methods.

Toward space-optimal approximate colored indexes at scale

This paper introduces Zindex, a space-efficient indexing framework for large-scale sequence repositories, achieving compact storage and fast query performance with novel interleaved filters and merging mechanisms.

spearfish: ultrafast Δ-mapping of long reads to redundant transcriptomes

spearfish improves long-read mapping efficiency by leveraging transcriptome redundancy, achieving faster speeds and lower memory usage than existing tools.

Theoretical prediction of assembly contiguity

The paper derives a formula (Z-value) to predict contig length from read length, coverage, and genome properties, showing high accuracy and practical applications for assembler choice and experimental design.

Towards a foundation model for raw nanopore signal through discrete tokenization

This paper introduces Brieno, a self-supervised model for raw nanopore signals that improves read classification and methylation detection without reference genomes.

Measuring satellite arrays of the human Y chromosome from sequencing reads

The paper introduces Yruler, a tool to measure Y chromosome satellite arrays from sequencing reads without alignment, revealing lineage-specific variations in satellite length and composition.

Short-read whole-genome sequencing identifies the Tg(Tal1-cre/ERT)42-056Jrg transgene insertion site on mouse chromosome 4

Provenance-aware handling of identical dengue genome records alters inferred envelope-protein variation in Bangladesh DENV-3

The paper evaluates how handling identical dengue genome records affects inferred envelope-protein variation in a Bangladesh DENV-3 dataset, showing that exclusion strategies can lead to loss of variation.

WheatPanRef: a unified linear pan-reference genome for wheat genomics

WheatPanRef provides a unified linear pan-reference genome for wheat, improving read alignment and enabling integration of genomic resources across diverse accessions.

NanoPAMDA enables rapid PAM characterization of metagenome-derived Cas9 effectors

The paper identifies novel Cas9 orthologs from metagenomic data and develops NanoPAMDA to rapidly characterize their PAM preferences.

Genomic prediction of resistance to Phytophthora megakarya in cacao from a sparse host-pathogen screen

This study predicts cacao resistance to Phytophthora megakarya using genomic data, finding that host genomic relationships are more predictive than pathogen relatedness in a structured host-pathogen system.

A Bias Correction Method for Substructure Estimation with Small Reference Sample Sizes

The paper evaluates how small reference sample sizes affect substructure estimation and proposes bias corrections for improved accuracy.

SQANTI-evidence: isoform-resolved, evidence-tiered structural annotation of unannotated genomes from long-read RNA-seq

SQANTI-evidence annotates genomes from long-read RNA-seq without a reference, achieving high precision in gene and isoform prediction across species.

An end-to-end in silico framework for truth-based validation and regression testing of clinical genome sequencing pipelines, from simulated reads to reportable findings

This paper introduces an end-to-end in silico framework to validate and test clinical genome sequencing pipelines from simulated reads to reportable findings using a fixed truth set.

Sourmash accurately profiles strains from long-read metagenomes preserving gene content

This study evaluates Sourmash's ability to profile microbial strains from long-read metagenomes, showing accurate gene content recovery and abundance estimation.

vafSOMA: Detecting cell-layer-fixed somatic mutations in plants

vafSOMA detects cell-layer-fixed somatic mutations in plants using tissue composition, improving mutation detection and rate estimation in bulk sequencing data.

A population-based resource for the prioritization of rare variants of unknown significance in clinical genomics

The paper identifies rare founder variants in a population and develops a platform for variant prioritization, showing that some pathogenic variants may be missed by conventional methods.

NPlasmid-seq: Cas9-encoded terminal signatures enable molecule-level nanopore quality control of vector and IVT-template plasmids

NPlasmid-seq detects sub-percent contamination and sequence heterogeneity in plasmid preparations using Cas9-encoded terminal signatures, revealing structural variants missed by consensus-based methods.

FastaGuard: FASTA preflight QC for modern bioinformatics pipelines

FastaGuard is a FASTA preflight QC tool that detects structural issues in assemblies and stops pipelines before expensive analysis, with high accuracy in identifying faults.

Variant Classification of a Non-Protein Coding Gene: ACMG/AMP Specifications for RMRP from the Clinical Genome Resource Severe Combined Immunodeficiency Disease Variant Curation Expert Panel

This paper adapts ACMG/AMP variant classification criteria for the non-protein-coding gene RMRP, resulting in a framework for classifying variants in cartilage-hair hypoplasia.

Engineering and characterisation of AAVS1 FRT cell lines for inducible and dose-dependent gene expression

This paper develops a stable RPE1 cell line with inducible and dose-dependent transgene expression using CRISPR/Cas9 and FRT/Tet-On systems, validated through multi-omics analysis.

Comparative genomics of canonical antifungal dsRNA target genes across fungal plant pathogens: conserved siRNA-length windows define the scope for broad-spectrum spray-induced gene silencing

This study evaluates the conservation of antifungal dsRNA target genes across fungal plant pathogens at siRNA-length resolution, finding limited conservation beyond closely related species.

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

Recurrent mitotic error and purifying selection shape chromosomal mosaicism across human tissues

This study identifies mosaic chromosomal alterations in healthy human tissues, revealing tissue-specific patterns of mitotic errors and purifying selection across aging.

Genetic and Epigenetic Landscape of Self-Identified Hispanics/Latino in All Of Us

The paper analyzes genetic variation, ancestry, and DNA methylation in Hispanic/Latino participants using long-read sequencing, identifying novel variants and phenotype associations.