rustybam : a composable toolkit for alignment analysis and visualization with SafFire

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ID: 337570
2026
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Abstract
SUMMARY: We present rustybam, a Rust-based command-line toolkit for CIGAR-aware manipulation of PAF and BAM alignments, and SafFire, a browser-based tool for interactive genome comparison visualization with annotation overlays. rustybam's composable subcommands provide overlap resolution, coordinate liftover, alignment splitting at structural variants, scaffolding, and identity statistics. AVAILABILITY AND IMPLEMENTATION: Both tools are open source under the MIT license. rustybam is available via Bioconda (https://anaconda.org/bioconda/rustybam), crates.io, and GitHub (https://github.com/vollgerlab/rustybam). SafFire is hosted at https://vollgerlab.com/SafFire/ with source code at https://github.com/vollgerlab/SafFire. Archived versions are available on Zenodo: rustybam (https://doi.org/10.5281/zenodo.4654875) and SafFire (https://doi.org/10.5281/zenodo.5765964). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Reference Key
openalex_W7224131998 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Cade Mirchandani, Mitchell Robert Vollger
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Journal BMC Bioinformatics
Year 2026
DOI
10.1093/bioinformatics/btag799
URL
https://doi.org/10.1093/bioinformatics/btag799
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