ArticleFrontiers in plant science2021
Comparison of Short-Read Sequence Aligners Indicates Strengths and Weaknesses for Biologists to Consider.
Article in Frontiers in plant science, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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
38 citing papers in PubMed, 63 citations in OpenAlex.
- Genomic Connectivity and Adaptive Gene Flow ofResearch square · 2026Article
- T-rex: standardized analysis of germline variants in whole-exome sequencing trios.Scientific reports · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Detection of alternative splicing: deep sequencing or deep learning?Briefings in bioinformatics · 2026Article
- Human Endogenous Retroviruses and Diseases.MedComm · 2025Review
- Benchmarking of low coverage sequencing workflows for precision genotyping in eggplant.BMC plant biology · 2025Article
- Combining panel-based and whole-transcriptome-based gene fusion detection by long-read sequencing.Cell reports methods · 2025Article
- Incorporating exon-exon junction reads enhances differential splicing detection.BMC bioinformatics · 2025Article
- Evaluating the Effectiveness of Various Small RNA Alignment Techniques in Transcriptomic Analysis by Examining Different Sources of Variability Through a Multi-Alignment Approach.Methods and protocols · 2025Article
- Bioinformatics perspectives on transcriptomics: A comprehensive review of bulk and single-cell RNA sequencing analyses.Quantitative biology (Beijing, China) · 2025Review
- Sensitivity of transcriptomics: Different samples and methodology alter conclusions in Gulf pipefish (Syngnathus scovelli).The Journal of heredity · 2025Article
- Multi-Omics Profiling of Lipid Variation and Regulatory Mechanisms in Poultry Breast Muscles.Animals : an open access journal from MDPI · 2025Article
- Article
- Skeletal Muscle mRNA Splicing Variants Association With Four Different Fitness and Energetic Measures in the GESTALT Study.Journal of cachexia, sarcopenia and muscle · 2025Article
- Article
- ChimericFragments: computation, analysis and visualization of global RNA networks.NAR genomics and bioinformatics · 2024Article
- Anchored-fusion enables targeted fusion search in bulk and single-cell RNA sequencing data.Cell reports methods · 2024Article
- Review
- Machine learning on alignment features for parent-of-origin classification of simulated hybrid RNA-seq.BMC bioinformatics · 2024Article
- Benchmarking RNA-Seq Aligners at Base-Level and Junction Base-Level Resolution Using thePlants (Basel, Switzerland) · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Aligning short-read sequences is the foundational step to most genomic and transcriptomic analyses, but not all tools perform equally, and choosing among the growing body of available tools can be daunting. Here, in order to increase awareness in the research community, we discuss the merits of common algorithms and programs in a way that should be approachable to biologists with limited experience in bioinformatics. We will only in passing consider the effects of data cleanup, a precursor analysis to most alignment tools, and no consideration will be given to downstream processing of the aligned fragments. To compare aligners [Bowtie2, Burrows Wheeler Aligner (BWA), HISAT2, MUMmer4, STAR, and TopHat2], an RNA-seq dataset was used containing data from 48 geographically distinct samples of the grapevine powdery mildew fungus
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.