Software & methodsSnakemake

OpusTaxa

One workflow for shotgun metagenomes, from raw reads to results

git clone https://github.com/yenkaiC/OpusTaxa

Shotgun metagenomics analyses usually mean stitching together a dozen tools, each with its own databases, formats and quirks. OpusTaxa wraps them in a single Snakemake workflow that runs the same way on a laptop or a SLURM cluster: download from the SRA, quality control, host read removal, taxonomic profiling with several complementary profilers, assembly and gene prediction, and functional and antimicrobial-resistance annotation.

Tools in the workflow

  • fastp
  • FastQC
  • MultiQC
  • Nonpareil
  • MetaPhlAn
  • Kraken2
  • Bracken
  • SingleM
  • Sylph
  • MetaSPAdes
  • Prodigal-GV
  • HUMAnN
  • RGI
  • antiSMASH

How to cite OpusTaxa

Chen Y-K, Harker CM, Pham CM, Grundy L, Wardill HR, Roach MJ, Ryan FJ. OpusTaxa: a unified workflow for taxonomic profiling, assembly, and functional analysis of shotgun metagenomes. bioRxiv. 2026. doi:10.64898/2026.04.15.718825

@article{chen2026opustaxa,
  title   = {OpusTaxa: A Unified Workflow for Taxonomic Profiling, Assembly, and Functional Analysis of Shotgun Metagenomes},
  author  = {Chen, Yen-Kai and Harker, C. M. and Pham, C. M. and Grundy, L. and Wardill, H. R. and Roach, M. J. and Ryan, Feargal J.},
  journal = {bioRxiv},
  year    = {2026},
  doi     = {10.64898/2026.04.15.718825}
}