perbase mit Homebrew installieren

Projektlinks

• Homepage
• Paketmanager-Seite

Befehle und Aliase

• perbase

Projektgeschichte

Seth Stadick created perbase as a highly parallel utility for per-position and per-nucleotide analysis of BAM and CRAM alignment data. The project emphasizes scalable concurrency and counting behavior intended to avoid accuracy problems identified in some existing depth tools.

Adoptionsgeschichte

The official project documents installation through Bioconda, Cargo, Homebrew, or downloadable release binaries, giving it several routes into genomics workflows.

Wie es verwendet wird

Commonly used to calculate nucleotide-resolved depth, restrict analysis to BED or VCF/BCF positions, account for overlapping mates, and emit compressed tabular output suitable for tabix indexing.

Warum Paket-Nerds sich dafür interessieren

It is a Rust-based genomics CLI distributed across both language-specific and scientific package ecosystems. Its explicit treatment of deletions, reference skips, mate overlap, compression, and indexing makes it interesting to users who care about reproducible low-level sequencing metrics.

Zeitleiste

• 2023: perbase 0.9.0 was used by the Nano-DMS-MaP project.
• Current project: Available through Bioconda, Cargo, Homebrew, and GitHub releases.

Related projects

• The official README compares aspects of its counting behavior with bam-readcount and sambamba.
• tabix is documented for indexing and querying compressed perbase output.

Quellen

• Official repository and README: https://github.com/sstadick/perbase