fastk ☆
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Description:
K-mer counter for high-fidelity shotgun datasets
Type: Formula  |  Latest Version: 1.1.0@0  |  Tracked Since: Dec 17, 2025
Links: Homepage  |  formulae.brew.sh
Category: Other
Tags: genomics bioinformatics kmer sequencing hifi
Install: brew install fastk
About:
FastK is a specialized k-mer counting tool optimized for high-fidelity (HiFi) long-read shotgun sequencing data. It efficiently processes large genomic datasets to generate accurate k-mer frequency profiles, which are essential for genome assembly, quality control, and analysis. Its performance makes it particularly valuable for modern PacBio HiFi datasets.
Key Features:
  • Optimized for high-fidelity (HiFi) long-read sequencing data
  • Memory-efficient k-mer counting algorithms
  • Generates standard k-mer frequency tables for downstream analysis
  • Fast processing speeds for large genomic datasets
Use Cases:
  • Pre-processing HiFi reads for genome assembly pipelines
  • Generating k-mer spectra for genome complexity analysis and quality control
  • Estimating genome size and heterozygosity from raw sequencing data
Alternatives:
  • jellyfish – General-purpose k-mer counter; FastK is more specialized for HiFi data performance
  • KMC – Another efficient k-mer counter; FastK offers specific optimizations for long-read datasets
License: BSD-3-Clause AND (MIT AND BSD-3-Clause) AND MIT
Dependencies: xz
Bottles available for: arm64_tahoe, arm64_sequoia, arm64_sonoma, arm64_ventura, sonoma, ventura, arm64_linux, x86_64_linux
Version History
Detected Version Rev Change Commit
Sep 13, 2025 6:24pm 0 VERSION_BUMP 41bbe0ec
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