ISAtools improves full-length RNA isoform analysis from long-read RNA sequencing
Long-read RNA sequencing has made it possible for researchers to study complete RNA molecules instead of assembling them from many short fragments. This provides a much clearer picture of how genes produce different RNA isoforms through alternative splicing. However, ...
Amaranth – enhanced single-cell transcript assembly via discriminative modelling of UMI reads and internal reads
Single-cell RNA sequencing has changed how scientists study biology by allowing them to measure gene activity in individual cells instead of averaging signals across millions of cells. This level of detail helps researchers better understand development, disease, and the ...
SLRanger – an integrated approach for spliced leader detection and operon prediction using long RNA reads
In many organisms, including simple animals like worms, genes are often arranged in clusters called operons. When these genes are copied into RNA, they need an extra step of processing called spliced leader (SL) trans-splicing. This process attaches a ...
IgSeqR – identification, assembly and characterization of tumor immunoglobulin transcripts from RNA sequencing data
Researchers at the University of Southampton have developed a cutting-edge tool that can rapidly identify and characterize tumor-related immunoglobulin genes directly from RNA sequencing (RNA-seq) data. This groundbreaking technique has the potential to significantly enhance our understanding of B ...
Uncalled4 – a toolkit for nanopore signal alignment, analysis and visualization
Nanopore sequencing has revolutionized the way scientists analyze DNA and RNA, allowing them to detect genetic sequences and modifications without extra processing steps. However, accurately identifying certain nucleotide modifications—especially in RNA—remains a challenge. A research team from Johns Hopkins ...
Semblans – automated assembly and processing of RNA-Seq data
With the rapid growth of RNA sequencing (RNA-seq) technologies, researchers now have access to vast amounts of short-read sequence data, enabling them to study gene expression in greater detail. However, analyzing this data to construct an accurate transcriptome – ...
Aletsch – accurate assembly of multiple RNA-seq samples
High-throughput RNA sequencing (RNA-seq) has revolutionized our ability to decode the activities of genes within cells. However, one persistent challenge has been reconstructing full-length...
GTax – improving de novo transcriptome assembly by removing foreign RNA contamination
The cost and complexity of generating a complete reference genome means that many organisms lack an annotated reference. An alternative is to use a de novo reference transcriptome. This technology is cost-effective but is susceptible to off-target RNA contamination. Researchers ...
ORFanage – investigating open reading frames in known and novel transcripts
Researchers at the Johns Hopkins University have developed ORFanage, a system designed to assign open reading frames (ORFs) to both known and novel gene transcripts while maximizing similarity to annotated proteins. The primary intended use...
transXpress – a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation
RNA-seq followed by de novo transcriptome assembly has been a transformative technique in biological research of non-model organisms, but the computational processing of RNA-seq data entails...
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Most Shared Posts
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- Upcoming Workshop – Advanced Topics in Single Cell RNA-Seq Analysis: Multiomics ATAC-Seq & RNA-Seq
- BAP-seq – bioorthogonal masked acylating agents for proximity-dependent RNA labelling
- Single-cell RNA-seq of the rare virosphere reveals the native hosts of giant viruses in the marine environment
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