LongRead Quality Control and Filtering Version 1
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Download RO CrateWorkflow for LongRead Quality Control and Filtering
- NanoPlot (read quality control) before and after filtering
- Filtlong (read trimming)
- Kraken2 taxonomic read classification before and after filtering
- Minimap2 read filtering based on given references
Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default
All tool CWL files and other workflows can be found here:
https://gitlab.com/m-unlock/cwl/workflows
How to setup and use an UNLOCK workflow:
https://m-unlock.gitlab.io/docs/setup/setup.html
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| identifier | identifier used | Identifier for this dataset used in this workflow |
|
| nanopore_reads | Nanopore reads | Nanopore sequence file locally fastq format |
|
| filter_references | Contamination reference file | Contamination references fasta file for contamination filtering |
|
| keep_reference_mapped_reads | Keep mapped reads | Keep with reads mapped to the given reference |
|
| kraken_database | Kraken2 database | Kraken2 database location, multiple databases is possible |
|
| threads | Number of threads | Number of threads to use for computational processes |
|
| memory | Maximum memory in MB | Maximum memory usage in megabytes |
|
| step | CWL base step number | Step number for order of steps |
|
| destination | Output Destination | Optional Output destination used for cwl-prov reporting. |
|
Steps
| ID | Name | Description |
|---|---|---|
| merge_nanopore_fastq | Merge fastq files | n/a |
| fastqc_nanopore_before | FastQC before | Quality assessment and report of reads before filter |
| prepare_bbmap_db | Prepare references | Prepare BBMap references to a single fasta file and unique headers |
| nanopore_array_to_file | array to file | Converts the file array to a single file object |
| nanopore_quality_kraken2 | Kraken2 | Taxonomic classification of FASTQ reads |
| nanopore_quality_kraken2_krona | Krona | Visualization of Kraken2 classification with Krona |
| reference_filter_nanopore | Reference mapping | Removal of contaminated reads using minimap2 mapping |
| fastqc_nanopore_after | FastQC after | Quality assessment and report of reads before filter |
| reports_files_to_folder | Reports to folder | Preparation of fastp output files to a specific output folder |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| reports_folder | Filtering reports folder | Folder containing all reports of filtering and quality control |
|
| filtered_reads | Filtered nanopore reads | Filtered nanopore reads |
|
Version History
Version 1 (earliest) Created 21st Apr 2022 at 17:19 by Bart Nijsse
Initial commit
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masterae127fa
Creators and Submitter
Views: 857
Created: 21st Apr 2022 at 17:19
Last updated: 7th Apr 2023 at 15:07
AttributionsNone
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https://orcid.org/0000-0001-8172-8981
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