ReviewBriefings in bioinformatics2022
A simple guide to de novo transcriptome assembly and annotation.
Review in Briefings in bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
86 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Comparative phytochemical profiling and meta‑analysis of public transcriptomic datasets uncover species‑ and organ‑specific patterns of flavonoid and phenolic biosynthesis in Ferula species.BMC plant biology · 2026Pooled it
- Physiological and Transcriptomic Responses to Cold Stress in Taiwan Loach (Antioxidants (Basel, Switzerland) · 2026Article
- Article
- Mucin-induced metabolic reprogramming inmSystems · 2026Article
- At the Edge of Survival: Exploring the Frontiers of Tardigrade Extreme Stress Tolerance.Molecular ecology · 2026Review
- Integrated morphological analyses of Cladomorphus phyllinus and transcriptomic analysis of Cladomorphus trimariensis provide insights into the cardiac morphophysiology of stick insects (Phasmida: Phasmatidae).Cell and tissue research · 2026Article
- Augmenting transcriptome annotations through the lens of splicing evolution.Genome research · 2026Article
- HyDRA: A pipeline for integrating long- and short-read RNAseq data for custom transcriptome assembly.iScience · 2026Article
- Identification of candidate genes governing key metabolic pathways in fenugreek (Trigonella spp.) through integrated transcriptomic and metabolomic analysis.Functional & integrative genomics · 2026Article
- Gene Expression and Structural Differences Underpinning Black and White Colouration in Spiders.Molecular ecology · 2026Article
- Transcriptome Profiling of Leaves and Roots from Rooibos (Plants (Basel, Switzerland) · 2026Article
- Computational identification and characterization of noncoding RNA-encoded peptides: tools, databases, and in silico strategies.Amino acids · 2026Review
- Functional transcriptomic analysis and drought-induced regulation of secondary metabolism in Artemisia ludoviciana Nutt.BMC plant biology · 2026Article
- Rapid phylogenomic analysis for viral surveillance and metagenomic profiling with Omni2Tree.bioRxiv : the preprint server for biology · 2026Article
- Comprehensive assessment of transcriptome assembly quality using CATS.Nature communications · 2026Article
- Metamorphosis and lncRNAs: A Close Relationship.Genesis (New York, N.Y. : 2000) · 2026Review
- The de novo transcriptome of the freshwater copepod Cyclops abyssorum tatricus reveals high-elevation adaptation.Scientific reports · 2026Article
- An ecology-driven microbial consortium enhances plant growth and immunity while sustaining rhizospheric microbial balance.Plant communications · 2026Article
- A systematic PCR-based framework for amplification of long and multi-exonic genes in non-model insects: : A case study of Bemisia tabaci Asia II 1.Molecular biology reports · 2026Article
- De novo transcriptome assembly of the Moroccan fir, Abies marocana Trab.Scientific data · 2026Article
26 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A transcriptome constructed from short-read RNA sequencing (RNA-seq) is an easily attainable proxy catalog of protein-coding genes when genome assembly is unnecessary, expensive or difficult. In the absence of a sequenced genome to guide the reconstruction process, the transcriptome must be assembled de novo using only the information available in the RNA-seq reads. Subsequently, the sequences must be annotated in order to identify sequence-intrinsic and evolutionary features in them (for example, protein-coding regions). Although straightforward at first glance, de novo transcriptome assembly and annotation can quickly prove to be challenging undertakings. In addition to familiarizing themselves with the conceptual and technical intricacies of the tasks at hand and the numerous pre- and post-processing steps involved, those interested must also grapple with an overwhelmingly large choice of tools. The lack of standardized workflows, fast pace of development of new tools and techniques and paucity of authoritative literature have served to exacerbate the difficulty of the task even further. Here, we present a comprehensive overview of de novo transcriptome assembly and annotation. We discuss the procedures involved, including pre- and post-processing steps, and present a compendium of corresponding tools.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.