Description:
Cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
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Type: Formula
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Latest Version: 2.12.0@0
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Tracked Since: Dec 4, 2025
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Links:
Homepage |
formulae.brew.sh
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Category: Other
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Tags:
bioinformatics
fasta
fastq
sequence-analysis
cli
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Install:
brew install seqkit
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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.
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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
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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
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Alternatives:
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bioawk
– Bioawk adds FASTA/Q parsing to awk, offering more flexibility for custom text processing but with a steeper learning curve.
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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.
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