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Daedalus v0.3.2.

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@feargalr feargalr released this 08 Feb 23:22
· 11 commits to main since this release
v0.3.2
9a16fef

Daedalus is a metagenomic analysis pipeline that assembles shotgun sequencing data, predicts microbial genes, and identifies exact matches to known immune epitopes. It is designed to detect potential T cell cross-reactive peptides.

Highlights

  • Added automatic skipping of completed pipeline steps (resume-safe execution)
  • Bundled filtered human-relevant IEDB epitope database for convenience
  • Improved installation layout (conda YAMLs, scripts directory)
  • Expanded and clarified documentation

New features

  • Daedalus now detects existing outputs and avoids re-running:
    • SRA download
    • Host read removal
    • Assembly
    • Gene prediction
  • This makes Daedalus robust to job preemption and incremental reruns on HPC systems

Database

  • Includes a filtered FASTA of human / human-associated epitopes from IEDB (late 2025)
  • Provided for convenience only — users should cite IEDB and original sources

Notes

  • Designed for paired-end Illumina shotgun metagenomic data
  • Assumes human host for read removal
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