Workflows

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 ...