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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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rustybam: a composable toolkit for alignment analysis and visualization with SafFire.
1Department of Human Genetics and Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA.
Biorxiv : the Preprint Server for Biology
|February 27, 2026
Summary
This study introduces rustybam, a command-line toolkit for manipulating sequence alignments (PAF and BAM), and SafFire, a visualization tool for genome comparisons. These open-source bioinformatics tools enhance genomic data analysis and visualization.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Accurate manipulation and visualization of large-scale genomic sequence alignments are crucial for advancing biological research.
- Existing tools often lack specialized functionalities for complex alignment tasks like structural variant analysis or interactive comparative genomics.
Purpose of the Study:
- To introduce rustybam, a novel Rust-based command-line toolkit for CIGAR-aware manipulation of PAF and BAM alignment files.
- To present SafFire, an interactive browser-based tool designed for visualizing and comparing genomes with integrated annotation overlays.
Main Methods:
- rustybam offers composable subcommands for operations including overlap resolution, coordinate liftover, alignment splitting at structural variants, scaffolding, and identity statistics.
- SafFire provides an intuitive web interface for genome comparison, supporting annotation overlays to facilitate detailed analysis.
Main Results:
- rustybam enables efficient and precise CIGAR-aware processing of sequence alignment data.
- SafFire facilitates interactive exploration and visual comparison of genomic datasets, enhancing the understanding of structural variations and annotations.
Conclusions:
- The developed tools, rustybam and SafFire, offer powerful and accessible solutions for advanced genomic data manipulation and visualization.
- These open-source bioinformatics resources are expected to streamline and improve the analysis pipelines for researchers in genomics and related fields.
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