Nanopore Assembly Workflow - Deprecated -
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Download RO Crate- 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
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| identifier | Identifier used | Identifier for this dataset used in this workflow |
|
| threads | Number of threads | Number of threads to use for computational processes |
|
| memory | Maximum memory in MB | Maximum memory usage in megabytes |
|
| nanopore_fastq_files | Nanopore reads | List of file paths with Nanopore raw reads in fastq format |
|
| illumina_forward_reads | illumina forward reads | illumina sequenced forward read file |
|
| illumina_reverse_reads | illumina reverse reads | illumina sequenced reverse file |
|
| use_reference_mapped_reads | Use mapped reads | Continue with reads mapped to the given reference |
|
| deduplicate | Deduplicate reads | Remove exact duplicate reads (Illumina) with fastp |
|
| kraken_database | Kraken2 database | Absolute path with database location of kraken2 |
|
| basecall_model | Basecalling model | Basecalling model used with Guppy |
|
| metagenome | When working with metagenomes | Metagenome option for the flye assembly |
|
| filter_references | Contamination reference file(s) | Reference fasta file(s) for contamination filtering |
|
| pilon_fixlist | Pilon fix list | A comma-separated list of categories of issues to try to fix |
|
| binning | Run binning workflow | Run with contig binning workflow |
|
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 |
|
| illumina_quality_stats | Filtered statistics | Statistics on quality and preprocessing of the reads |
|
| kraken2_output | Kraken2 reports | Kraken2 taxonomic classification reports |
|
| assembly_output | Assembly output | Output from different assembly steps |
|
| binning_output | Binning output | Binning outputfolders |
|
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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Version-2441b6ec
Version 1 (earliest) Created 6th Jan 2022 at 07:38 by Jasper Koehorst
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Creators and Submitter
Views: 1478
Created: 6th Jan 2022 at 07:38
Last updated: 2nd Feb 2023 at 15:16
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