🧬 First Public Pannotator Release

Overview

First release of the Pannotator tool. It provides a single entry point that executes the full workflow, essentially following Bakta's approach. This includes:

• Protein-coding gene search, clustering using mmseqs2, with subsequent functional annotation.
• Parallel tRNA, tmRNA, rRNA and ncRNA genes annotation.
• Pseudogene search.
• sORF, oriC/oriV/oriT prediction.
• Feature filtering.

Installation

Nextflow version >=21.04.0 is required to run the Pannotator pipeline. Based on your execution environment, select the profile from the provided options described in the features section.

Features

• Automatic Bakta database download if none provided or found in the default directory.
• --save_intermediate flag that facilitates debugging or individual step output exploration.
• Execution profiles inherited from the base configuration by the Wellcome Sanger Institute's PaM department:
  • local
  • docker
  • singularity
  • conda
  • standard (enables Singularity and uses LSF as the executor)

Contributors

• @d-goryslavets
• @t3tianaa
• @alnf
• @flass