perbase ☆
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Description:
Fast and correct perbase BAM/CRAM analysis
Type: Formula  |  Tracked Since: Dec 28, 2025
Links: Homepage  |  formulae.brew.sh
Category: Other
Tags: bioinformatics genomics bam cram sequencing analysis
Install: brew install perbase
About:
Perbase is a command-line tool designed for rapid and accurate per-base analysis of BAM and CRAM alignment files. It efficiently calculates depth, base quality, and other metrics while correctly handling paired-end reads and duplicate marking. The tool provides a robust alternative to traditional scripts, offering improved performance and correctness for genomic data processing.
Key Features:
  • High-performance processing of large BAM/CRAM files
  • Correctly handles paired-end reads and duplicates
  • Outputs detailed per-base metrics including depth and quality
  • Memory-efficient streaming architecture
Use Cases:
  • Generating per-base depth files for variant calling pipelines
  • Quality control of sequencing alignment data
  • Creating pileup summaries for genomic regions
Alternatives:
  • samtools depth – Samtools is a standard tool but Perbase offers faster performance and more accurate handling of certain edge cases like overlapping paired-end reads.
  • bedtools coverage – Bedtools is versatile for interval operations, whereas Perbase is specialized for high-speed per-base metrics directly from alignment files.
Version History
Detected Version Rev Change Commit
Sep 29, 2025 1:01am 0 VERSION_BUMP 8e672384
Sep 28, 2025 11:19pm 0 VERSION_BUMP c3feb2be
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