ArticleGenome biology2019
Alevin efficiently estimates accurate gene abundances from dscRNA-seq data.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 166 papers.
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Who cites it
166 citing papers in PubMed.
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- QCatch: a framework for quality control assessment and analysis of single-cell sequencing data.Bioinformatics (Oxford, England) · 2026Article
- Preterm birth skews the developmental trajectory of myeloid-derived suppressor cells in the first 48 hours of life: single-cell transcriptomics and inferred intercellular communication.Molecular medicine (Cambridge, Mass.) · 2026Article
- BenchDrop-seq: a microfluidics-free platform for benchtop single-cell long-read RNA sequencing.bioRxiv : the preprint server for biology · 2026Article
- A high-resolution atlas of the brain predicts lineage and birth order underlying neuronal identity.Cell genomics · 2026Article
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- Single cell transcriptomics of human weight loss links adipocyte NPY1R to control of lipolysis.Molecular metabolism · 2026Article
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- Sustained diabetes remission induced by FGF1 involves a shift in transcriptionally distinct AgRP neuron subpopulations.Molecular metabolism · 2026Article
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- Host Genetic Architecture between Epstein-Barr Virus Activity and Multiple Sclerosis Reveals Shared Pathways.medRxiv : the preprint server for health sciences · 2025Article
- Derepression of the epithelial transcription factor GRHL2 promotes direct hepatocyte-to-cholangiocyte transdifferentiation.PLoS biology · 2025Article
106 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
Abstract
We introduce alevin, a fast end-to-end pipeline to process droplet-based single-cell RNA sequencing data, performing cell barcode detection, read mapping, unique molecular identifier (UMI) deduplication, gene count estimation, and cell barcode whitelisting. Alevin's approach to UMI deduplication considers transcript-level constraints on the molecules from which UMIs may have arisen and accounts for both gene-unique reads and reads that multimap between genes. This addresses the inherent bias in existing tools which discard gene-ambiguous reads and improves the accuracy of gene abundance estimates. Alevin is considerably faster, typically eight times, than existing gene quantification approaches, while also using less memory.
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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.