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Namaste 🙏

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How to use 📖

To learn more about how to use the workflow, see the user manual.

What it does 

flowchart LR
    A[Raw reads] -->|Preprocess:  fastplong| B(High-quality reads)
    B -->|Assembly: metaFlye| C(Contigs)
    B -->|Screen ARMs: MetaPointFinder| M(Reads with resistance mutations)
    M -->|Map to: minimap2| C(Contigs)
    C -->|Screen ARGs: KMA/ResFinder| D(ARG-containing contigs)
    D -->|Mask: BEDtools| E(Masked contigs)
    E -->|Classify: Centrifuger| F(Taxonomy-assigned contigs)
    C -->|Predict plasmids: geNomad| G(Plasmid/virus/chromosome contigs)

The workflow works as follows:

  1. Preprocess reads

  2. Assemble metagenomes

  3. Screen for presence of antibiotic resistance genes

  4. Also screen for antibiotic resistance mutations

  5. Classify contigs taxonomically

  6. Predict whether contigs derive from chromosomes, plasmids or viruses

And comes with several additional functions, like automated downloading of reference databases and combining resistome data in comprehensive CSV-formatted tables.

What it creates

For an overview of the output files that are created in the process, please consult output files.