Research Object Crate for (Hybrid) Metagenomics workflow

**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 quality report) (optional) - Workflow binnning https://workflowhub.eu/workflows/64?version=11 - Metabat2/MaxBin2/SemiBin - DAS Tool - CheckM - BUSCO - GTDB-Tk - (optional) - Workflow bin annotation (https://workflowhub.eu/workflows/1170) - bakta - KoFam scan (optional) - Interpro Scan(optional) - eggNOG mapper (optional) - Workflow SAPP conversion (optional, default on) (https://workflowhub.eu/workflows/1174/) (optional) - Workflow Genome-scale metabolic models from bins https://workflowhub.eu/workflows/372 - CarveMe (GEM generation) - MEMOTE (GEM test suite) - SMETANA (Species METabolic interaction ANAlysis) Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default

**All tool CWL files and other workflows can be found here:**
Tools: https://gitlab.com/m-unlock/cwl/-/tree/master/cwl
Workflows: https://gitlab.com/m-unlock/cwl/-/tree/master/cwl/workflows
**How to setup and use an UNLOCK workflow:**
https://m-unlock.gitlab.io/docs/setup/setup.html

Author

Bart Nijsse, Jasper Koehorst, Changlin Ke

License

Apache-2.0

Contents