ArticleG3 (Bethesda, Md.)2020
Evaluation of STAR and Kallisto on Single Cell RNA-Seq Data Alignment.
Article in G3 (Bethesda, Md.), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 58 citations in OpenAlex.
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- 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
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- Bioinformatics perspectives on transcriptomics: A comprehensive review of bulk and single-cell RNA sequencing analyses.Quantitative biology (Beijing, China) · 2025Review
- Transcriptomic signatures of prostate cancer progression: a comprehensive RNA-seq study.3 Biotech · 2025Article
- Unlocking hematopoietic stem cell potential: integrative computational approaches for genomic and transcriptomic analysis.Frontiers in cell and developmental biology · 2025Review
- nf-core/marsseq: systematic preprocessing pipeline for MARS-seq experiments.Bioinformatics advances · 2025Article
- Characterization of Loss-of-Imprinting in Breast Cancer at the Cellular Level by Integrating Single-Cell Full-Length Transcriptome with Bulk RNA-Seq Data.Biomolecules · 2024Article
- Uncovering functional lncRNAs by scRNA-seq with ELATUS.Nature communications · 2024Article
- Split Pool Ligation-based Single-cell Transcriptome sequencing (SPLiT-seq) data processing pipeline comparison.BMC genomics · 2024Article
- A Multi-Omics Analysis Revealed the Diversity of the MYB Transcription Factor Family's Evolution and Drought Resistance Pathways.Life (Basel, Switzerland) · 2024Article
- Article
- Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references.Nature methods · 2023Article
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- Computationally Efficient Assembly of Pseudomonas aeruginosa Gene Expression Compendia.mSystems · 2023Article
- Schlafen 12 Slows TNBC Tumor Growth, Induces Luminal Markers, and Predicts Favorable Survival.Cancers · 2023Article
- Pseudoalignment tools as an efficient alternative to detect repeated transposable elements in scRNAseq data.Bioinformatics (Oxford, England) · 2023Article
- Digits in a dish: AnFrontiers in cell and developmental biology · 2023Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Alignment of scRNA-Seq data are the first and one of the most critical steps of the scRNA-Seq analysis workflow, and thus the choice of proper aligners is of paramount importance. Recently, STAR an alignment method and Kallisto a pseudoalignment method have both gained a vast amount of popularity in the single cell sequencing field. However, an unbiased third-party comparison of these two methods in scRNA-Seq is lacking. Here we conduct a systematic comparison of them on a variety of Drop-seq, Fluidigm and 10x genomics data, from the aspects of gene abundance, alignment accuracy, as well as computational speed and memory use. We observe that STAR globally produces more genes and higher gene-expression values, compared to Kallisto, as well as Bowtie2, another popular alignment method for bulk RNA-Seq. STAR also yields higher correlations of the Gini index for the genes with RNA-FISH validation results. Using 10x genomics PBMC 3K scRNA-Seq and mouse cortex single nuclei RNA-Seq data, STAR shows similar or better cell-type annotation results, by detecting a larger subset of known gene markers. However, the gain of accuracy and gene abundance of STAR alignment comes with the price of significantly slower computation time (4 folds) and more memory (7.7 folds), compared to Kallisto.
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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.