SEEK ID: https://workflowhub.eu/people/227
Location: Not known
ORCID: https://orcid.org/0000-0002-5516-8391
Joined: 6th Jan 2022
Expertise: Not specified
Tools: Not specified
Related items
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 ...
Type: Common Workflow Language
Creators: Bart Nijsse, Jasper Koehorst, Germán Royval
Submitter: Bart Nijsse
- 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 ...
Type: Common Workflow Language
Creators: Bart Nijsse, Jasper Koehorst, Germán Royval
Submitter: Jasper Koehorst
- deprecated -
Workflow for sequencing with ONT Nanopore, from basecalling to assembly.
- Guppy (basecalling of raw reads)
- MinIONQC (quality check)
- FASTQ merging from multi into one file
- Kraken2 (taxonomic classification)
- Krona (classification visualization)
- Flye (de novo assembly)
- Medaka (assembly polishing)
- QUAST (assembly quality reports)
All tool CWL files and other workflows can be found here: Tools: https://git.wur.nl/unlock/cwl/-/tree/master/cwl Workflows: ...
Type: Common Workflow Language
Creators: Bart Nijsse, Jasper Koehorst, Germán Royval
Submitter: Jasper Koehorst