Workflow for microbial (meta-)genome annotation

Input is a (meta)genome sequence in fasta format.

• bakta

• KoFamScan (optional)

• InterProScan (optional)

• eggNOG mapper (optional)

• To RDF conversion with SAPP (optional, default on) --> SAPP conversion Workflow in WorkflowHub

git: https://gitlab.com/m-unlock/cwl

Workflow for Metagenomics binning from assembly.

Minimal inputs are: Identifier, assembly (fasta) and an associated sorted BAM file

Summary

• MetaBAT2 (binning)
• MaxBin2 (binning)
• SemiBin2 (binning)
• Binette (bin merging)
• EukRep (eukaryotic classification)
• CheckM2 (bin completeness and contamination)
• BUSCO (bin completeness)
• GTDB-Tk (bin taxonomic classification)
• CoverM (bin abundances)

Including: Bin annotation (workflow: https://workflowhub.eu/workflows/1170):

• Bakta

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