Nanopore Guppy Basecalling Assembly Workflow Version 1
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Workflow for sequencing with ONT Nanopore, from basecalling to assembly.
- Guppy (basecalling of raw reads)
- MinIONQC (quality check)
- FASTQ merging from multi into one file
- Kraken2 (taxonomic classification)
- Krona (classification visualization)
- Flye (de novo assembly)
- Medaka (assembly polishing)
- QUAST (assembly quality reports)
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
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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 |
|
| fast5_files | nanopore reads | folder with Nanopore raw reads |
|
| configuration_command | n/a | n/a |
|
| kraken_database | n/a | database location of kraken2 |
|
| basecall_model | basecalling model | basecalling model used with Guppy |
|
Steps
| ID | Name | Description |
|---|---|---|
| workflow_basecalling | Guppy-CPU basecalling | Basecalling with Guppy for CPU of raw reads to FASTQ reads with summary |
| workflow_nanopore_noguppy | Nanopore workflow | The rest of the nanopore workflow without basecalling |
| guppy_files_to_folder | Guppy output folder | Preparation of Guppy output files to a specific output folder |
| workflow_minionqc | MinIONQC quality check | Plots and statistics generated with MinIONQC from basecalling with Guppy |
| minionqc_files_to_folder | MinIONQC output folder | Preparation of MinIONQC output files to a specific output folder |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| guppy_output | Guppy for CPU | Basecalling of raw reads with Guppy |
|
| minionqc_output | MinION-Quality-Check | Quality check of basecalling with MinIONQC |
|
| merge_output | FASTQ files merged | Concatenation of FASTQ files from Guppy |
|
| kraken2_output | Kraken2 reports | Kraken2 taxonomic classification reports |
|
| krona_output | Krona taxonomy visualization | Visual presentation in HTML of Kraken2 results |
|
| flye_output | Flye de novo assembler for single-molecule reads | Flye output directory |
|
| medaka_output | Medaka polisher | Polishing of Flye assembly |
|
| quast_output | QUAlity assessment | QUAST analysis output |
|
Version History
Version 1 (earliest) Created 6th Jan 2022 at 07:36 by Jasper Koehorst
Added/updated 1 files
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Views: 5513 Downloads: 761
Created: 6th Jan 2022 at 07:36
Last updated: 2nd Nov 2022 at 15:03
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Teams: UNLOCK, Systems and Synthetic Biology
Organizations: UNLOCK, Wageningen University & Research
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Teams: UNLOCK, Systems and Synthetic Biology
Organizations: UNLOCK, Wageningen University & Research
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