Nanopore Assembly Workflow - Deprecated -
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Download RO-CrateWorkflow for sequencing with ONT nanopore, from basecalling to assembly quality. Steps:
- Kraken2 (taxonomic classification of FASTQ reads)
- Krona (classification visualization)
- Flye (de novo assembly)
- Medaka (assembly polishing)
- QUAST (assembly quality reports)
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 |
|
| threads | number of threads | number of threads to use for computational processes |
|
| nanopore_fastq_reads | nanopore FASTQ reads | file of FASTQ reads |
|
| kraken_database | n/a | full pathway with database location of kraken2 |
|
| basecall_model | basecalling model | basecalling model used with Guppy |
|
Steps
| ID | Name | Description |
|---|---|---|
| concatenate | n/a | n/a |
| workflow_kraken2 | Taxonomic classification with Kraken2 | Taxonomic classification of FASTQ reads |
| kraken_compress | n/a | n/a |
| 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 |
| 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 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| kraken2_output | Kraken2 reports | Kraken2 taxonomic classification reports |
|
| 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 3 (latest) Created 20th Apr 2022 at 10:12 by Jasper Koehorst
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master69b53ab
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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master
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Creators and Submitter
Views: 3805 Downloads: 587
Created: 6th Jan 2022 at 07:38
Last updated: 2nd Feb 2023 at 15:16
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