Workflow Type: Common Workflow Language

- 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:

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?
memory Maximum memory in MB Maximum memory usage in megabytes
  • int?
nanopore_fastq_files Nanopore reads List of file paths with Nanopore raw reads in fastq format
  • string[]?
illumina_forward_reads illumina forward reads illumina sequenced forward read file
  • string[]?
illumina_reverse_reads illumina reverse reads illumina sequenced reverse file
  • string[]?
use_reference_mapped_reads Use mapped reads Continue with reads mapped to the given reference
  • boolean
deduplicate Deduplicate reads Remove exact duplicate reads (Illumina) with fastp
  • boolean?
kraken_database Kraken2 database Absolute path with database location of kraken2
  • string
basecall_model Basecalling model Basecalling model used with Guppy
  • string
metagenome When working with metagenomes Metagenome option for the flye assembly
  • boolean?
filter_references Contamination reference file(s) Reference fasta file(s) for contamination filtering
  • string[]
pilon_fixlist Pilon fix list A comma-separated list of categories of issues to try to fix
  • string
binning Run binning workflow Run with contig binning workflow
  • boolean?

Steps

ID Name Description
workflow_quality_nanopore Nanopore quality and filtering workflow Quality and filtering workflow for nanopore reads
workflow_quality_illumina Illumina quality and filtering workflow Quality and filtering workflow for illumina reads
nanopore_kraken2 Kraken2 Nanopore Taxonomic classification of Nanopore reads
illumina_kraken2 Kraken2 Illumina Taxonomic classification of FASTQ reads
kraken2_compress Compress kraken2 Compress large kraken2 report file
kraken2_krona Krona Kraken2 Visualization of kraken2 with Krona
flye Nanopore Flye assembly De novo assembly of single-molecule reads with Flye
medaka Medaka polishing of assembly Medaka for polishing of assembled genome
metaquast_medaka assembly evaluation evaluation of polished assembly with metaQUAST
workflow_pilon Pilon worklow Illumina reads assembly polishing with Pilon
metaquast_nanopore_pilon Illumina assembly evaluation Illumina evaluation of pilon polished assembly with metaQUAST
illumina_pilon_readmapping Read mapping Illumina read mapping on pilon assembly for binning
illumina_pilon_sam_to_sorted_bam sam conversion to sorted bam Sam file conversion to a sorted bam file
workflow_binning Binning workflow Binning workflow to create bins
kraken2_files_to_folder Kraken2 output folder Preparation of Kraken2 output files to a specific output folder
flye_files_to_folder Flye output folder Preparation of Flye output files to a specific output folder
metaquast_medaka_files_to_folder Nanopore metaQUAST output folder Preparation of metaQUAST output files to a specific output folder
medaka_files_to_folder Medaka output folder Preparation of Medaka output files to a specific output folder
metaquast_pilon_files_to_folder Illumina metaQUAST output folder Preparation of QUAST output files to a specific output folder
pilon_files_to_folder Pilon output folder Preparation of pilon output files to a specific output folder
assembly_files_to_folder Flye output folder Preparation of Flye output files to a specific output folder
binning_files_to_folder Binning output folder Preparation of quast output files to a specific output folder

Outputs

ID Name Description Type
nanopore_quality_output Read quality and filtering reports Quality reports
  • Directory
illumina_quality_stats Filtered statistics Statistics on quality and preprocessing of the reads
  • Directory
kraken2_output Kraken2 reports Kraken2 taxonomic classification reports
  • Directory
assembly_output Assembly output Output from different assembly steps
  • Directory
binning_output Binning output Binning outputfolders
  • Directory

Version History

Version 3 (latest) Created 20th Apr 2022 at 10:12 by Jasper Koehorst

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

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Created: 6th Jan 2022 at 07:38

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