Workflow (hybrid) metagenomic assembly and binning + GEMs

Accepts both Illumina and Nanopore

• Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1

• Workflow LongRead Quality: https://workflowhub.eu/workflows/337

• Kraken2 taxonomic classification of FASTQ reads

• SPAdes/Flye (Assembly)

• QUAST (Assembly quality report)

Workflow binnning https://workflowhub.eu/workflows/64?version=11 (optional)

• Metabat2/MaxBin2/SemiBin
• DAS Tool
• CheckM
• BUSCO
• GTDB-Tk ...

Workflow for Metagenomics binning from assembly

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

Summary

• MetaBAT2 (binning)
• MaxBin2 (binning)
• SemiBin (binning)
• DAS Tool (bin merging)
• EukRep (eukaryotic classification)
• CheckM (bin completeness and contamination)
• BUSCO (bin completeness)
• GTDB-Tk (bin taxonomic classification)

Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default

**All tool CWL ...