ArticleNature methods2017
Simulation-based comprehensive benchmarking of RNA-seq aligners.
Article in Nature methods, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 143 papers.
What it found
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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.
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Who cites it
143 citing papers in PubMed.
- The degree and direction of subgenome expression bias in Brassica napus vary between cultivars, tissues and developmental stages.The Plant journal : for cell and molecular biology · 2026Article
- PanGraphRNA: An efficient and flexible bioinformatics platform for graph pangenome-based RNA-seq data analysis.Journal of integrative plant biology · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- DeepSAP: improved RNA-seq alignment by integrating transcriptome guidance with transformer-based splice junction scoring.Genome biology · 2026Article
- RNA-SeqEZPZ: a point-and-click pipeline for comprehensive transcriptomics analysis with interactive visualizations.GigaScience · 2026Article
- NEXT-scASV: a Nextflow pipeline for allele-specific variant calling from single-cell RNA-seq data.GigaScience · 2026Article
- Detection of alternative splicing: deep sequencing or deep learning?Briefings in bioinformatics · 2026Article
- A plant-derived antimicrobial peptide with multiple mechanisms of action exhibiting antibacterial and antibiofilm activities comparable to or superior to polymyxin B.Current research in microbial sciences · 2026Article
- Modelling APOL1-mediated kidney inflammation and fibrosis using a partially reprogrammed urine-derived SIX2-positive renal progenitor cell line.Stem cell research & therapy · 2025Article
- Preventing effect of plant extracts and omega-3 on age-related cognitive decline in male mice.Brain, behavior, & immunity - health · 2025Article
- Brain transcriptomics highlight abundant gene expression and splicing alterations in non-neuronal cells in aFTLD-U.Acta neuropathologica · 2025Article
- HDAC inhibition unlocks tumor plasticity and enhances immunotherapy response in Myc-Driven Small Cell Lung Cancer.bioRxiv : the preprint server for biology · 2025Article
- Incorporating exon-exon junction reads enhances differential splicing detection.BMC bioinformatics · 2025Article
- Defactinib in Combination with Mitotane Can Be an Effective Treatment in Human Adrenocortical Carcinoma.International journal of molecular sciences · 2025Article
- Aging Alters mRNA Processing in the Mouse Ovary.Cells · 2025Article
- The effect of prolonged G-quadruplex stabilization on the functions of human cells.Scientific reports · 2025Article
- A dataset of tissue-specific gene expression dynamics during seed development in Brassica.Scientific data · 2025Article
- The impact of glucocorticoid receptor transactivation on context-dependent cell migration dynamics.Scientific reports · 2025Article
- Complementary Strategies to Identify Differentially Expressed Genes in the Choroid Plexus of Patients with Progressive Multiple Sclerosis.Neuroinformatics · 2025Article
- Contrasting and combining transcriptome complexity captured by short and long RNA sequencing reads.Genome research · 2024Article
83 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
6 authors.
Funding
Abstract
Alignment is the first step in most RNA-seq analysis pipelines, and the accuracy of downstream analyses depends heavily on it. Unlike most steps in the pipeline, alignment is particularly amenable to benchmarking with simulated data. We performed a comprehensive benchmarking of 14 common splice-aware aligners for base, read, and exon junction-level accuracy and compared default with optimized parameters. We found that performance varied by genome complexity, and accuracy and popularity were poorly correlated. The most widely cited tool underperforms for most metrics, particularly when using default settings.
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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.