Workflow (hybrid) metagenomic assembly and binning

• Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1
• FastQC (control)
• fastp (quality trimming)
• kraken2 (taxonomy)
• bbmap contamination filter
• Kraken2 taxonomic classification of FASTQ reads
• SPAdes (Assembly)
• QUAST (Assembly quality report)
• BBmap (Read mapping to assembly)
• Workflow binnning https://workflowhub.eu/workflows/64?version=11
• Metabat2
• CheckM
• BUSCO
• GTDB-Tk

**All tool CWL files and other ...

Workflow for Metagenomics from raw reads to annotated bins. Summary

• MetaBAT2 (binning)
• CheckM (bin completeness and contamination)
• GTDB-Tk (bin taxonomic classification)
• BUSCO (bin completeness)

All tool CWL files and other workflows can be found here: Tools: https://git.wur.nl/unlock/cwl/-/tree/master/cwl Workflows: https://git.wur.nl/unlock/cwl/-/tree/master/cwl/workflows

The dependencies are either accessible from https://unlock-icat.irods.surfsara.nl (anonymous,anonymous) and/or ...