variant calling

Genomes2Genes converts Progressive Cactus alignments into validated gene-level alignments, identifying de novo genes and enabling evolutionary analysis.

This paper improves SBWT-based k-mer indexes by making them faster and smaller through batching, prefetching, and orientation optimization, outperforming SSHash in speed and space efficiency.

This paper introduces a variant filtering framework called SMART filtering to improve diagnostic outcomes in genome sequencing by prioritizing non-coding and regulatory variants.

The paper characterizes genetic variation in the bovine sialic acid network across European and South African cattle breeds, identifying 15 prioritized protein-altering variants and highlighting population differences.

TurboANI is a fast, homology-aware ANI estimator with up to ~40,000x speedup over alignment-based methods and better accuracy than FastANI and skani.

The paper shows that the source of annotation data significantly affects the quality of automatically reconstructed genome-scale metabolic models.

This study estimates mutation and recombination rates in polar bears using whole-genome sequencing, finding species-specific values that improve demographic inference for conservation.

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

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

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

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.

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.

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.

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

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.

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.

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

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

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.

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.

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

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

The paper presents 25 new microsporidian genomes, revealing extreme pangenome diversity and novel tetraploid structures in some species.

This paper identifies genomic loci and mutations associated with DDT metabolic resistance in Anopheles gambiae using bulk segregant analysis and confirms their selection in natural populations.

The paper analyzes the structure and evolution of a selfish centromere in monkeyflowers, identifying genomic expansions and gene content differences that may contribute to meiotic drive.

The paper presents a high-quality crabeater seal reference genome and shows it has high genetic diversity, low inbreeding, and a history of population expansion.