Workflows

Workflow for short paired end reads quality control, trimming and filtering. Multiple paired datasets will be merged into single paired dataset. Summary:

• Sequali QC on raw data files
• fastp for read quality trimming
• BBduk for phiX and rRNA filtering (optional)
• Filter human reads using Hostile (optional)
• Custom read filtering using Hostile (optional)
• Sequali QC on filtered (merged) data

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

Workflow (hybrid) metagenomic assembly and binning

• Workflow Illumina Quality:
• Sequali (control)
• hostile contamination filter
• fastp (quality trimming)
• Workflow Longread Quality:
• NanoPlot (control)
• fastplong (quality trimming)
• hostile contamination filter
• Kraken2 taxonomic classification of FASTQ reads
• SPAdes/Flye (Assembly)
• Medaka/PyPolCA (Assembly polishing)
• QUAST (Assembly quality report)

(optional)

• Workflow binnning
• Metabat2/MaxBin2/SemiBin
• Binette
• BUSCO

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