Nanopore Guppy Basecalling Assembly Workflow
Version 1

Workflow Type: Common Workflow Language

- 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: https://git.wur.nl/unlock/cwl/-/tree/master/cwl/workflows

Click and drag the diagram to pan, double click or use the controls to zoom.

Inputs

ID Name Description Type
identifier identifier used Identifier for this dataset used in this workflow
  • string
threads number of threads number of threads to use for computational processes
  • int?
fast5_files nanopore reads folder with Nanopore raw reads
  • File[]
configuration_command n/a n/a
  • string
kraken_database n/a database location of kraken2
  • Directory
basecall_model basecalling model basecalling model used with Guppy
  • string

Steps

ID Name Description
workflow_basecalling Guppy-CPU basecalling Basecalling with Guppy for CPU of raw reads to FASTQ reads with summary
workflow_nanopore_noguppy Nanopore workflow The rest of the nanopore workflow without basecalling
guppy_files_to_folder Guppy output folder Preparation of Guppy output files to a specific output folder
workflow_minionqc MinIONQC quality check Plots and statistics generated with MinIONQC from basecalling with Guppy
minionqc_files_to_folder MinIONQC output folder Preparation of MinIONQC output files to a specific output folder

Outputs

ID Name Description Type
guppy_output Guppy for CPU Basecalling of raw reads with Guppy
  • Directory
minionqc_output MinION-Quality-Check Quality check of basecalling with MinIONQC
  • Directory
merge_output FASTQ files merged Concatenation of FASTQ files from Guppy
  • Directory
kraken2_output Kraken2 reports Kraken2 taxonomic classification reports
  • Directory
krona_output Krona taxonomy visualization Visual presentation in HTML of Kraken2 results
  • Directory
flye_output Flye de novo assembler for single-molecule reads Flye output directory
  • Directory
medaka_output Medaka polisher Polishing of Flye assembly
  • Directory
quast_output QUAlity assessment QUAST analysis output
  • Directory

Version History

Version 1 (earliest) Created 6th Jan 2022 at 07:36 by Jasper Koehorst

Added/updated 1 files


Open master 62ee0fe
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Views: 3466   Downloads: 245

Created: 6th Jan 2022 at 07:36

Last updated: 2nd Nov 2022 at 15:03

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