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
• Workflow Longread Quality:
• NanoPlot (control)
• filtlong (quality trimming)
• kraken2 (taxonomy)
• minimap2 contamination filter
• Kraken2 taxonomic classification of FASTQ reads
• SPAdes/Flye (Assembly)
• Pilon/Medaka/PyPolCA (Assembly polishing)
• QUAST (Assembly ...

- Deprecated -

See our updated hybrid assembly workflow: https://workflowhub.eu/workflows/367

And other workflows: https://workflowhub.eu/projects/16#workflows

Workflow for sequencing with ONT Nanopore data, from basecalled reads to (meta)assembly and binning

• Workflow Nanopore Quality
• Kraken2 taxonomic classification of FASTQ reads
• Flye (de-novo assembly)
• Medaka (assembly polishing)
• metaQUAST (assembly quality reports)

When Illumina reads are provided:

• Workflow ...

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 ...