kallisto ☆
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Description:
Quantify abundances of transcripts from RNA-Seq data
Type: Formula  |  Tracked Since: Dec 28, 2025
Links: Homepage  |  formulae.brew.sh
Category: Other
Tags: bioinformatics rna-seq transcriptomics quantification genomics
Install: brew install kallisto
About:
Kallisto is a fast and accurate RNA-seq quantification program that uses a novel algorithm called pseudoalignment. It directly analyzes read data without the need for time-consuming alignment, enabling rapid abundance estimation of transcripts. This tool significantly reduces computational requirements while maintaining high accuracy for gene expression analysis.
Key Features:
  • Ultra-fast transcript quantification using pseudoalignment
  • Low memory footprint and CPU usage
  • Accurate abundance estimates without read alignment
  • Support for single-end and paired-end reads
  • Bootstrap sampling for uncertainty estimation
Use Cases:
  • Quantifying transcript abundance from RNA-seq data
  • Differential expression analysis workflows
  • Single-cell RNA-seq analysis
  • Metatranscriptomic studies
Alternatives:
  • Salmon – Similar pseudoalignment approach with additional bias correction features
  • STAR + featureCounts – Traditional alignment-based method, slower but provides aligned BAM files
Version History
Detected Version Rev Change Commit
Feb 28, 2026 1:20pm 0 REVISION_ONLY 6dc87956
Jan 22, 2026 1:07am 2 REVISION_ONLY 5a159202
Sep 13, 2025 4:07pm 1 VERSION_BUMP 4e27bf7d
Dec 22, 2024 6:49pm 1 VERSION_BUMP 54782326
Sep 27, 2024 10:13am 1 VERSION_BUMP 85085b96
Sep 14, 2024 8:48am 0 VERSION_BUMP 3be05c12
Jul 21, 2024 11:42am 0 VERSION_BUMP 3493bfd2
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