Workflow for nanopore read quality control and contamination filtering.
- FastQC before filtering (read quality control)
- Kraken2 taxonomic read classification
- Minimap2 read filtering based on given references
- FastQC after filtering (read quality control)
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
WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default ...
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: