LongRead Quality Control and Filtering
Version 1

Workflow Type: Common Workflow Language
Work-in-progress

Workflow 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

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
  • string
nanopore_reads Nanopore reads Nanopore sequence file locally fastq format
  • File[]
filter_references Contamination reference file Contamination references fasta file for contamination filtering
  • File[]?
keep_reference_mapped_reads Keep mapped reads Keep with reads mapped to the given reference
  • boolean
kraken_database Kraken2 database Kraken2 database location, multiple databases is possible
  • Directory[]?
threads Number of threads Number of threads to use for computational processes
  • int?
memory Maximum memory in MB Maximum memory usage in megabytes
  • int?
step CWL base step number Step number for order of steps
  • int?
destination Output Destination Optional Output destination used for cwl-prov reporting.
  • string?

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
  • Directory
filtered_reads Filtered nanopore reads Filtered nanopore reads
  • File

Version History

Version 1 (earliest) Created 21st Apr 2022 at 17:19 by Bart Nijsse

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Views: 1696   Downloads: 131

Created: 21st Apr 2022 at 17:19

Last updated: 7th Apr 2023 at 15:07

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