Nanopore Assembly Workflow - Deprecated -
Version 3 (latest)

Version 3 (latest)

Version 2

Version 1 (earliest)

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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:

Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1
Assembly polishing with Pilon
Workflow binnning https://workflowhub.eu/workflows/64?version=11
- Metabat2
- CheckM
- BUSCO
- GTDB-Tk

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.

SEEK ID: https://workflowhub.eu/workflows/254?version=3

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