long-read sequencing

CLCluster: a redundancy-reduction contrastive learning-based clustering method of cancer subtype based on multi-omics data

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.

Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotype and phenotype in chronic lymphocytic leukemia

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

Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity

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'.

Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing

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.

Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle

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

Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease

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.

An ultraconserved snoRNA-like element in long noncoding RNA CRNDE promotes ribosome biogenesis and cell proliferation

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

TeloSearchLR: an algorithm to detect novel telomere repeat motifs using long sequencing reads

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

What is the correct genomic structure of the complex chromosomal rearrangement at the Fm locus in Silkie chicken?

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, a rapid and accurate tool to demultiplex direct RNA nanopore sequencing datasets

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

SQANTI-reads: a tool for the quality assessment of long read data in multi-sample lrRNA-seq experiments.

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

Cas9-based enrichment for targeted long-read metabarcoding

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: a multi-sample motif discovery and visualization tool for tandem repeats

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: Improving long-read structural variant discovery and genotyping with local haplotype modeling

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

Realfreq: Real-time base modification analysis for nanopore sequencing

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

Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment

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

Chromosome-level genome assembly of a doubled haploid brook trout (Salvelinus fontinalis)

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: precise, read-level genotyping of short tandem repeats using long reads and single-nucleotide variation

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

Development of ferret immune repertoire reference resources and single-cell-based high-throughput profiling assays

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

The positionally conserved long non-coding RNA DANCR is an essential regulator of zebrafish development and a human melanoma oncogene

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.

Kudoa genomes from contaminated hosts reveal extensive gene order conservation and rapid sequence evolution

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

A rapid approach for linear epitope vaccine profiling reveals unexpected epitope tag immunogenicity

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.

FULL-LENGTH HYBRID TRANSCRIPTOME OF THE OLFACTORY ROSETTE IN SENEGALESE SOLE (Solea senegalensis): AN ESSENTIAL GENOMIC RESOURCE TO IMPROVE REPRODUCTION AT FARMS

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.

Analysis of 30 chromosome-level Drosophila genome assemblies reveals dynamic evolution of centromeric satellite repeats

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: An integrated platform for simulating transcriptomic reads with realistic PCR error representation across various RNA sequencing technologies

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

A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines

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

Large diversity in the O-chain biosynthetic cluster within populations ofPelagibacterales

The paper examines O-chain polysaccharide biosynthesis cluster diversity in Pelagibacterales using SAGs and long-read metagenomics, finding high diversity and limited recent horizontal gene transfer.

DiMeLo-cito: a one-tube protocol for mapping protein-DNA interactions reveals CTCF bookmarking in mitosis

DiMeLo-cito improves DiMeLo-seq by eliminating wash steps, enabling mitotic protein-DNA interaction analysis in diploid human cells and revealing CTCF bookmarking.

The complete genome sequence of the crayfish pathogen Candidatus Paracoxiella cheracis n.g. n.sp. provides insight into pathogenesis and the phylogeny of the Coxiellaceae family

This paper reports the complete genome of Candidatus Paracoxiella cheracis, revealing insights into its pathogenesis and phylogeny within the Coxiellaceae family.

Mapler: Assessing assembly quality in taxonomically rich metagenomes sequenced with HiFi reads

Mapler evaluates Hi-Fi long read metagenome assemblies, providing metrics to assess quality and identify bottlenecks in genome reconstruction.