2 items tagged with 'binning'.
Work-in-progress
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
- Kraken2 taxonomic classification of FASTQ reads
- SPAdes (Assembly)
- QUAST (Assembly quality report)
- BBmap (Read mapping to assembly)
- Workflow binnning https://workflowhub.eu/workflows/64?version=11
- Metabat2
- CheckM
- BUSCO
- GTDB-Tk
**All tool CWL files and other ...
Created: 14th Jun 2022 at 09:14, Last updated: 14th Jun 2022 at 10:19
Work-in-progress
Workflow for Metagenomics from raw reads to annotated bins. Summary
- MetaBAT2 (binning)
- CheckM (bin completeness and contamination)
- GTDB-Tk (bin taxonomic classification)
- BUSCO (bin completeness)
All tool CWL files and other workflows can be found here: Tools: https://git.wur.nl/unlock/cwl/-/tree/master/cwl Workflows: https://git.wur.nl/unlock/cwl/-/tree/master/cwl/workflows
The dependencies are either accessible from https://unlock-icat.irods.surfsara.nl (anonymous,anonymous) and/or ...
Created: 15th Oct 2020 at 14:55, Last updated: 29th Apr 2022 at 09:45