Nanopore Assembly Workflow - Deprecated -
Version 1 (earliest)

Version 3 (latest)

Version 2

Version 1 (earliest)

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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:

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SEEK ID: https://workflowhub.eu/workflows/254?version=1

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

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

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