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:


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


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


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: 2311   Downloads: 35

Created: 6th Jan 2022 at 07:36

Last updated: 2nd Nov 2022 at 15:03

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