samtools ☆
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Description:
Tools for manipulating next-generation sequencing data
Type: Formula  |  Tracked Since: Dec 16, 2025
Links: Homepage  |  formulae.brew.sh
Category: Other
Tags: bioinformatics genomics sequencing bam samtools
Install: brew install samtools
About:
Samtools is a suite of utilities for manipulating alignments in the SAM (Sequence Alignment/Map), BAM, and CRAM formats. It provides high-performance commands for sorting, indexing, variant calling, and pileup generation. It is an essential tool for bioinformaticians working with high-throughput sequencing data.
Key Features:
  • Format conversion between SAM, BAM, and CRAM
  • Indexing and random access to large alignment files
  • Utilities for sorting, filtering, and flagging alignments
  • Pileup generation and basic variant calling
Use Cases:
  • Indexing BAM files for rapid data retrieval in genome browsers
  • Filtering sequencing reads by mapping quality or flags
  • Converting large SAM files to compressed BAM for storage efficiency
Alternatives:
  • picard – Java-based alternative with similar functionality but higher memory overhead
  • bedtools – Better suited for genomic interval arithmetic and overlap analysis
Version History
Detected Version Rev Change Commit
Dec 16, 2025 5:11pm 0 VERSION_BUMP 9a254da4
Sep 26, 2025 5:16pm 0 VERSION_BUMP b934d5dd
Sep 16, 2025 12:32am 0 VERSION_BUMP 2d18239e
Sep 12, 2024 10:11pm 0 VERSION_BUMP e41fe19e
Sep 10, 2024 11:36pm 0 VERSION_BUMP 82b835b5
Apr 16, 2024 12:19am 0 VERSION_BUMP 5f97752d
Jan 24, 2024 4:55pm 0 VERSION_BUMP 0a0ce3dd
Jan 24, 2024 10:00am 0 VERSION_BUMP b5eccd9f
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