seqkit ☆
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Description:
Cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
Type: Formula  |  Latest Version: 2.12.0@0  |  Tracked Since: Dec 4, 2025
Links: Homepage  |  formulae.brew.sh
Category: Other
Tags: bioinformatics fasta fastq sequence-analysis cli
Install: brew install seqkit
About:
SeqKit is a command-line tool written in Go that provides a suite of utilities for manipulating FASTA and FASTQ files. It enables bioinformaticians to perform operations like searching, filtering, splitting, and shuffling with exceptional speed and low memory usage. Its cross-platform support and consistent interface make it a robust alternative to slower, script-based solutions.
Key Features:
  • Ultrafast processing with low memory footprint
  • Comprehensive subcommands for searching, splitting, and formatting
  • Cross-platform support (Linux, macOS, Windows)
  • Support for both FASTA and FASTQ formats
  • Stream processing for large datasets
Use Cases:
  • Filtering sequence data based on ID lists or length thresholds
  • Converting between FASTA and FASTQ formats or reformatting headers
  • Splitting large files into smaller chunks for parallel processing
  • Searching for specific sequences or patterns within datasets
Alternatives:
  • bioawk – Bioawk adds FASTA/Q parsing to awk, offering more flexibility for custom text processing but with a steeper learning curve.
  • seqtk – Seqtk is a popular tool for similar tasks but is written in C; SeqKit often provides a more intuitive interface and more built-in subcommands.
Version History
Detected Version Rev Change Commit
Dec 4, 2025 2:55am 0 VERSION_BUMP ee1ac3bd
Dec 4, 2024 6:08am 0 VERSION_BUMP a74ea9bf
Dec 4, 2024 12:52am 0 VERSION_BUMP 16f97f83
Sep 14, 2024 5:38pm 0 VERSION_BUMP 7fa1e0c8
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