porTraits workflow

Description:

The porTraits workflow annotates microbial sequences (MAGs or genomes) with phenotypic trait predictions using published tools. It assigns NCBI and GTDB taxonomy and pulls the respective records from the metaTraits database for context so that users can assess whether predicted traits are common or unusual.

For more details and to report issues, visit the GitHub porTraits GitHub repository . This workflow is powered by CloWM CloWM , the Cloud-based Workflow Manager, and can also be executed on the CloWM platform.

Analysis steps:

  • Gene calling: predicts coding sequences with prodigal.
  • Functional annotation: builds KEGG Ortholog (KO) and PFAM profiles with eggNOG‑mapper.
  • Trait prediction: integrates multiple genome‑based tools, BacDive‑AI, GenomeSPOT, Traitar, and MICROPHERRET, to infer microbial phenotypic traits.
  • Taxonomy assignment: runs GTDB‑Tk (GTDB r220) and reCOGnise to obtain GTDB and NCBI taxonomy.
  • Context in metaTraits: links results to closely related records in the metaTraits database for comparison.

Upload a genome:

porTraits is designed for high-quality MAGs and genomes, so lower-quality data may fail or yield sparse annotations. Typical runs take 1–3 hours, and outputs remain available for download for 24 hours. 'Try it out' to see example inputs and outputs.

Allowed extensions: .fa, .fasta, .fna and their gzipped variants (.fa.gz, .fasta.gz, .fna.gz). Maximum file size: 10 MB
Try it out