Workflow Type: Common Workflow Language

This is the nested workflow of the "parent" nanopore workflow without the guppy basecalling step

Workflow for sequencing with ONT nanopore, from basecalling to assembly quality. Steps:

  • Kraken2 (taxonomic classification of FASTQ reads)
  • Krona (classification visualization)
  • Flye (de novo assembly)
  • Medaka (assembly polishing)
  • QUAST (assembly quality reports)

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?
nanopore_fastq_reads nanopore FASTQ reads file of FASTQ reads
  • File[]
kraken_database n/a full pathway with database location of kraken2
  • Directory
basecall_model basecalling model basecalling model used with Guppy
  • string

Steps

ID Name Description
concatenate n/a n/a
workflow_kraken2 Taxonomic classification with Kraken2 Taxonomic classification of FASTQ reads
workflow_krona taxonomic classification visualization visualization of taxonomic classification with Krona
workflow_flye de novo assembly de novo assembly of single-molecule reads with Flye
workflow_medaka polishing of assembly Medaka for polishing of assembled genome
workflow_quast assembly evaluation evaluation of polished assembly qith QUAST
kraken2_files_to_folder Kraken2 output folder Preparation of Kraken2 output files to a specific output folder
krona_files_to_folder Krona output folder Preparation of Krona output files to a specific output folder
flye_files_to_folder Flye output folder Preparation of Flye output files to a specific output folder
medaka_files_to_folder Medaka output folder Preparation of Medaka output files to a specific output folder
quast_files_to_folder QUAST output folder Preparation of QUAST output files to a specific output folder

Outputs

ID Name Description Type
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 3 (latest) Created 20th Apr 2022 at 10:12 by Jasper Koehorst

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Version 2 Created 7th Jan 2022 at 09:32 by Jasper Koehorst

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Frozen Version-2 441b6ec

Version 1 (earliest) Created 6th Jan 2022 at 07:38 by Jasper Koehorst

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Created: 6th Jan 2022 at 07:38

Last updated: 2nd Feb 2023 at 15:16

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