Research Object Crate for (Hybrid) Metagenomics workflow

**Workflow (hybrid) metagenomic assembly and binning**
- Workflow Illumina Quality: [https://workflowhub.eu/workflows/336](https://workflowhub.eu/workflows/336) - Sequali (control) - hostile contamination filter - fastp (quality trimming) - Workflow Longread Quality: [https://workflowhub.eu/workflows/337](https://workflowhub.eu/workflows/337) - 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: [https://workflowhub.eu/workflows/64](https://workflowhub.eu/workflows/64) - Metabat2/MaxBin2/SemiBin - Binette - BUSCO - GTDB-Tk (optional) - MAG annotation: [https://workflowhub.eu/workflows/1170](https://workflowhub.eu/workflows/1170) - Bakta - Eggnog - InterProScan - Kofamscan - SAPP (to RDF) conversion (optional) - Workflow Genome-scale metabolic models [https://workflowhub.eu/workflows/372](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:**
https://gitlab.com/m-unlock/cwl/
**How to setup and use an UNLOCK workflow:**
https://docs.m-unlock.nl/docs/workflows/setup.html

Author

Bart Nijsse, Jasper Koehorst, Changlin Ke

License

Apache-2.0

Contents