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

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.