Latest updates for Transcriptome Assembly Tools

Fresh curated links around Transcriptome Assembly Tools are collected here so marketers can spot useful updates and turn timely ideas into posts faster.

Recent items include:

  • Amaranth – enhanced single-cell transcript assembly via discriminative modelling of UMI reads and internal reads
  • ISAtools improves full-length RNA isoform analysis from long-read RNA sequencing
  • Benchmarking long-read RNA sequencing tools for single-cell and spatial transcriptomics

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rna-seqblog.com /1 month ago

Amaranth – enhanced single-cell transcript assembly via discriminative modelling of UMI reads and internal reads

Amaranth improves transcript reconstruction from RNA sequencing data by modeling different read types, enabling more accurate isoform analysis at single-cell resolution...

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rna-seqblog.com /1 month ago

ISAtools improves full-length RNA isoform analysis from long-read RNA sequencing

RNA sequencing with ISAtools enables accurate reconstruction and quantification of full-length RNA isoforms while efficiently processing large PacBio sequencing datasets...

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rna-seqblog.com /1 month ago

Benchmarking long-read RNA sequencing tools for single-cell and spatial transcriptomics

RNA sequencing benchmark compares long-read bioinformatics tools for single-cell and spatial transcriptomics, helping researchers improve isoform detection and gene...

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rna-seqblog.com /2 weeks ago

PotatoRTD and TomatoRTD: comprehensive reference transcript datasets for accurate transcriptome analysis and isoform dis...

RNA sequencing and Iso-Seq improve potato and tomato transcript annotations, revealing additional isoforms and enabling more accurate analysis of gene expression and alternative sp...

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rna-seqblog.com /3 weeks ago

Tidesurf improves RNA velocity analysis for modern single-cell RNA sequencing

Tidesurf improves RNA sequencing analysis by accurately quantifying spliced and unspliced transcripts across 3' and 5' protocols for more reliable RNA velocity estimates...

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rna-seqblog.com /4 weeks ago

NextLongIso – a comprehensive Nextflow pipeline for multi-dimensional long-read RNA-seq analysis

NextLongIso provides a unified RNA sequencing pipeline for analyzing transcript isoforms, alternative splicing, promoter usage, and...

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journals.plos.org /1 month ago

Accurate <i>de novo</i> transcription unit annotation from run-on and sequencing data

by Paul R. Munn, Jay Chia, Charles G. Danko Functional element annotations are critical tools used to provide insight into the molecular processes governing cell development, diff...

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rna-seqblog.com /1 week ago

Ultrafast and reference-free sequence discovery in single-cell data

Malva enables ultrafast, reference-free searches across massive single-cell RNA sequencing datasets for mutations, splice junctions, pathogens, transcripts, and other sequence-leve...

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rna-seqblog.com /2 weeks ago

An end-to-end computational framework for “Record-seq” transcriptional recording data

A new framework adapts RNA sequencing analysis for Record-seq, improving spacer extraction, transcription-unit quantification, normalization, differential expression, and modeling...

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rna-seqblog.com /1 month ago

Spatial transcriptomics benchmark compares leading platforms

RNA sequencing and spatial transcriptomics were combined to benchmark leading platforms, helping researchers compare how accurately each maps gene activity within complex tissues.....

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rna-seqblog.com /1 month ago

STGBench – sequencing-level spatial DNA-RNA simulation for multimodal and virtual cell-oriented benchmarking of genomic...

STGBench generates realistic paired DNA and RNA sequencing datasets with known genetic alterations, enabling accurate benchmarking of spatial genomics and transcriptomics analysis....

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rna-seqblog.com /3 weeks ago

New RNA sequencing model improves sequencing depth planning for UMI transcriptomics

RNA sequencing model NB-Lib predicts sequencing depth requirements from shallow pilot data while accounting for library complexity, amplification differences, and molecular recover...

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rna-seqblog.com /1 month ago

NanoncRNA-seq – an rRNA-depleted full-length transcriptome strategy for identification of novel lncRNA isoforms

A new RNA sequencing workflow using nanopore technology improves full-length lncRNA isoform discovery, revealing many previously undetected transcripts missed by conventional short...

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journals.plos.org /1 week ago

ASPIRE: Accurate alternative splicing prediction from limited RNA sequencing data and a minimal gene set

by Ran Eisenberg, Efraim Rahamim, Eli Kopel, Miri Danan-Gotthold, Erez Y. Levanon, Ofir Lindenbaum Alternative splicing is a fundamental biological mechanism that increases protei...

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rna-seqblog.com /1 month ago

Seq-Scope-X pushes spatial transcriptomics beyond optical resolution

RNA sequencing combined with tissue expansion enabled ultra-high-resolution spatial transcriptomics, allowing researchers to map gene activity within individual cells with...

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rna-seqblog.com /3 weeks ago

From bench to bytes: a practical guide to RNA sequencing data analysis

A practical guide helps molecular biologists understand RNA sequencing data analysis, from quality control and normalization to differential expression and biological interpretatio...

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lifespan.io /1 month ago

A New Transcriptomic Clock for Intervention Analysis

A team of researchers has developed Pasta, a transcriptomic clock that accurately predicts the age-related effects of various compounds and gene expressions. Epigenetics versus tra...

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journals.plos.org /1 day ago

Not every gene is special: Modelling scale controls the false discovery rate when analysing high-throughput sequencing d...

by Scott J. Dos Santos, Andreea C. Murariu, Justin D. Silverman, Gregory B. Gloor Differential expression/abundance analyses are commonplace in studies employing high-throughput s...

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rna-seqblog.com /4 weeks ago

Machine learning improves RNA sequencing annotation of active genes

Machine learning improves interpretation of RNA sequencing data, helping researchers accurately identify active genes, non-coding RNAs, and other transcription units...

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rna-seqblog.com /1 month ago

DeepDETAILS – high-resolution reconstruction of cell-type-specific transcriptional regulatory processes from bulk sequen...

DeepDETAILS combines artificial intelligence with RNA sequencing and chromatin data to reconstruct cell-specific gene regulation from bulk tissue sequencing experiments...

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rna-seqblog.com /1 month ago

The Lomb–Scargle periodogram-based differentially expressed gene detection along pseudotime

RNA sequencing combined with a new computational method improved detection of genes that change during cellular transitions, helping researchers better understand...

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rna-seqblog.com /3 weeks ago

MitoClipSplice – machine learning improves RNA sequencing analysis of mitochondrial RNA processing

RNA sequencing combined with machine learning identifies mitochondrial RNA cleavage sites from soft-clipped reads, providing a new approach for investigating mitochondrial RNA...

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journals.plos.org /4 weeks ago

REvolutionH-tl 2.0: A fast and robust tool for decoding evolutionary gene histories

by José Antonio Ramírez-Rafael, Annachiara Korchmaros, Katia Aviña-Padilla, Alitzel López-Sánchez, Gabriel Martinez-Medina, Alfredo J. Hernández-Álvarez, Marc Hellmuth, Peter F. St...

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genengnews.com /1 week ago

Spatial Transcriptomics Tools May Link Tumor Organization to Treatment Response

A new spatial transcriptomics framework compares tumor “floor plans." In a study of 262 solid tumors, the team identified recurring spatial groups that may connect spatial structur...

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