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

Vollger, M. R.

2026-02-17 bioinformatics
10.64898/2026.02.16.706142 bioRxiv
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SummaryWe 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. rustybams composable subcommands provide overlap resolution, coordinate liftover, alignment splitting at structural variants, scaffolding, and identity statistics. Availability and implementationBoth 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.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.