jellyfish ☆
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Description:
Fast, memory-efficient counting of DNA k-mers
Type: Formula  |  Tracked Since: Dec 28, 2025
Links: Homepage  |  formulae.brew.sh
Category: Other
Tags: bioinformatics genomics k-mer sequencing dna command-line
Install: brew install jellyfish
About:
Jellyfish is a command-line tool for counting k-mers in DNA and RNA sequences with high performance. It utilizes a compact data structure to minimize memory usage while processing large sequencing files. This makes it ideal for genome assembly and other bioinformatics tasks requiring efficient k-mer analysis.
Key Features:
  • Memory-efficient counting using a compact hash table
  • Parallel processing support for multi-core systems
  • Supports both counting and querying of k-mers
  • Fast processing of large FASTA/FASTQ files
Use Cases:
  • Generating k-mer frequency tables for genome assembly
  • Estimating genome size and heterozygosity from sequencing data
  • Identifying unique or repetitive sequences in large datasets
Alternatives:
  • KMC – Another efficient k-mer counter, often faster on very large datasets but with a different interface
  • Khmer – Focuses on k-mer counting and filtering for large datasets, often used in assembly pipelines
Version History
Detected Version Rev Change Commit
Sep 12, 2025 2:37pm 0 VERSION_BUMP 76e6d17b
Sep 14, 2024 9:39am 0 VERSION_BUMP da7181ac
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