bowtie2 ☆
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Description:
Fast and sensitive gapped read aligner
Type: Formula  |  Latest Version: 2.5.4@0  |  Tracked Since: Dec 17, 2025
Links: Homepage  |  formulae.brew.sh
Category: Other
Tags: bioinformatics genomics alignment sequencing cli
Install: brew install bowtie2
About:
Bowtie2 is an ultra-fast and memory-efficient tool for aligning sequencing reads to large reference genomes. It employs an FM-index search strategy, allowing it to handle both short and long reads with high sensitivity. Its efficiency makes it a standard choice for high-throughput genomic analysis pipelines.
Key Features:
  • Ultra-fast alignment using FM-index
  • Supports gapped alignment with SIMD optimizations
  • Memory-efficient design suitable for large genomes
  • Handles both paired-end and unpaired reads
Use Cases:
  • Aligning DNA sequencing reads to a reference genome
  • Variant calling and genomic analysis workflows
  • Transcriptome alignment for RNA-seq studies
Alternatives:
  • BWA – BWA is another popular aligner, often preferred for slightly different read types or specific sensitivity requirements.
  • STAR – STAR is optimized specifically for RNA-seq splice-aware alignment, whereas Bowtie2 is more general-purpose.
License: GPL-3.0-or-later
Bottles available for: arm64_tahoe, arm64_sequoia, arm64_sonoma, arm64_ventura, arm64_monterey, sonoma, ventura, monterey, arm64_linux, x86_64_linux
Version History
Detected Version Rev Change Commit
Sep 11, 2025 11:30am 0 VERSION_BUMP 8cbe78c1
Sep 11, 2024 10:33am 0 VERSION_BUMP 4f8ec8d5
May 18, 2024 1:11am 0 VERSION_BUMP 8d8c5836
Oct 14, 2023 9:44pm 0 VERSION_BUMP 10e45d04
Sep 30, 2023 7:14am 0 VERSION_BUMP 705a78b0
Jan 18, 2023 6:06am 0 VERSION_BUMP 8a39552d
Jan 18, 2023 6:06am 0 VERSION_BUMP d9d7e55e
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