long-read sequencing

This study uses Nanopore DRS to show m6A modification on HBV RNA enhances stability by protecting long poly(A) tails, supporting m6A as an antiviral target.

GLASS filters erroneous splice-aware alignments from long-read RNA-seq data, improving transcriptome reconstruction accuracy across multiple species.

This study shows stochastic variation in virulence gene expression in T. cruzi helps diversify infection and evade immune recognition.

This paper introduces a method called kanpig for accurately genotyping structural variants using long-read alignment pileups, achieving higher concordance than existing tools.

CLCluster uses contrastive learning with multi-omics data to cluster cancer subtypes, showing improved performance over existing methods and identifying AS events linked to patient survival.

This study uses long-read scRNA-seq to analyze cancer subclone-specific mutations and transcriptomic differences in CLL patients with BTKC481S mutations.

Biosurfer identifies sources of protein isoform diversity by analyzing long-read RNA-seq data, revealing common mechanisms like alternative transcription start sites and 'ragged codons'.

This study uses direct RNA nanopore sequencing to analyze allele-specific pre-mRNA maturation in human lymphoblastoid cell lines, revealing splicing order differences and SNP-splicing associations.

The paper identifies a structural variant upstream of KIT associated with facial depigmentation in white-headed cattle using pangenome analysis and long-read sequencing.

The paper integrates long-read sequencing and gene expression to prioritize functional structural variants and tandem repeats in rare disease patients, identifying potential causal variants in a neurodevelopmental disorder.

The paper identifies an ultraconserved snoRNA-like element in the lncRNA CRNDE that promotes ribosome biogenesis and cell proliferation in renal cell carcinoma.

TeloSearchLR identifies novel telomere repeat motifs using long sequencing reads, improving detection in cases where short-read tools fail.

The paper reanalyzes a chicken genome assembly to correct a previously reported complex chromosomal rearrangement at the Fm locus, showing *Fm_2 is correct instead of *Fm_1 due to assembly errors.

SeqTagger demultiplexes direct RNA nanopore sequencing datasets with high precision and recall, supporting multiple chemistries and library types.

SQANTI-reads assesses long-read RNA-seq data quality using SQANTI3 metrics, identifying under-annotated genes and splicing site variation across samples.

This paper introduces a Cas9-based method for targeted long-read metabarcoding, enabling multiplexed enrichment of marker genes without PCR, and demonstrates its effectiveness in characterizing complex microbial and nematode communities.

MotifScope identifies and visualizes tandem repeats in population context using a de novo k-mer approach, outperforming existing tools in motif discovery and representation.

Sawfish improves long-read structural variant calling accuracy by modeling local haplotypes, outperforming existing tools in benchmark tests and joint-genotyping analyses.

Realfreq provides real-time base modification analysis for nanopore sequencing, enabling live data analysis during sequencing.

Uncalled4 improves nanopore signal alignment for DNA and RNA modification detection, identifying more modifications than existing tools in human cell lines.

The paper presents a chromosome-level genome assembly for brook trout using Hi-C and long-read sequencing, achieving high contiguity and annotation coverage.

STRkit is a software tool for accurate STR genotyping using long reads and single-nucleotide variants, achieving high F1 scores and Mendelian inheritance rates.

The paper develops ferret immune repertoire reference resources and assays using long-read transcriptome sequencing and genome annotation.

This study identifies DANCR as a conserved lncRNA essential for zebrafish development and a human melanoma oncogene, showing its role in regulating gene expression and promoting cancer progression.

This paper presents two new Kudoa genomes assembled from contaminated fish samples, revealing conserved gene order and rapid sequence evolution despite genomic simplification.

The paper presents a method using phage-displayed oligo pools and Nanopore sequencing to profile linear epitopes in a vaccine, revealing unexpected immunogenicity of epitope tags.

The paper generates a full-length transcriptome of the olfactory rosette in Senegalese sole, identifying known and novel transcripts to support reproductive management in aquaculture.

The paper analyzes 30 chromosome-level Drosophila genome assemblies to study the evolutionary dynamics of centromeric satellite repeats and identifies the ananassae subgroup as a model for centromere evolution.

Tresor simulates transcriptomic reads with PCR error representation across sequencing technologies, showing cell-type-specific profiles similar to reference data after duplicate removal.

This study benchmarks Nanopore long read RNA sequencing in human cell lines, showing improved isoform resolution compared to short reads.