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 ...

Runs MetaPhlAn 4 and HUMAnN 3

• Optional short read quality control workflow (https://workflowhub.eu/workflows/336)
• Includes renormalizing and all regroupings to other functional categories (EC,KO.. etc)

Required inputs are paired end reads and databases

Workflow for Metagenomics binning from assembly.

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

Summary

• MetaBAT2 (binning)
• MaxBin2 (binning)
• SemiBin2 (binning)
• Binette (bin merging)
• EukRep (eukaryotic classification)
• CheckM2 (bin completeness and contamination)
• BUSCO (bin completeness)
• GTDB-Tk (bin taxonomic classification)
• CoverM (bin abundances)

Including: Bin annotation (workflow: https://workflowhub.eu/workflows/1170):

• Bakta

...

Workflow for quality assessment of paired reads and classification using NGTax 2.0 and functional annotation using picrust2.
In addition files are exported to their respective subfolders for easier data management in a later stage.

Steps:

• Quality plots (FastQC)
• NG-TAX 2 High-throughput Amplicon Analysis
• PICRUSt 2 - Function prediction from marker gene sequences
• Export module for ngtax

Workflow for quality assessment and taxonomic classification of amplicon long read sequences. In addition files are exported to their respective subfolders for easier data management in a later stage.

Inputs are expected to be basecalled fastq files

Steps:

• NanoPlot read quality control, before and after filtering
• fastplong read quality and length filtering
• Emu abundance; species-level taxonomic abundance for full-length 16S read

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

...

Workflow for microbial (meta-)genome annotation

Input is a (meta)genome sequence in fasta format.

• bakta

• KoFamScan (optional)

• InterProScan (optional)

• eggNOG mapper (optional)

• To RDF conversion with SAPP (optional, default on) --> SAPP conversion Workflow in WorkflowHub

git: https://gitlab.com/m-unlock/cwl

Workflow for converting (genome) annotation tool output into a GBOL RDF file (TTL/HDT) using SAPP

Current formats / tools:

• EMBL format
• InterProScan (JSON/TSV)
• eggNOG-mapper (TSV)
• KoFamScan (TSV)

git: https://gitlab.com/m-unlock/cwl

SAPP (Semantic Annotation Platform with Provenance):
https://gitlab.com/sapp
https://academic.oup.com/bioinformatics/article/34/8/1401/4653704

Workflow for LongRead Quality Control and Filtering

• NanoPlot (read quality control) before and after filtering
• Filtlong (read trimming)
• Kraken2 taxonomic read classification before and after filtering
• Minimap2 read filtering based on given references

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

All tool CWL files and other workflows can be found here: https://gitlab.com/m-unlock/cwl/workflows

**How to setup and use an UNLOCK ...

- 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 ...