LongRead Quality Control and Filtering
Version 1

Workflow Type: Common Workflow Language
Work-in-progress

Workflow for LongRead Quality Control and Filtering

  • FastQC before filtering (read quality control)
  • Filtlong (read trimming)
  • Kraken2 taxonomic read classification
  • Minimap2 read filtering based on given references
  • FastQC after filtering (read quality control)

Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default

All tool CWL files and other workflows can be found here:
Tools: https://gitlab.com/m-unlock/cwl
Workflows: 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
  • 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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Created: 21st Apr 2022 at 17:19

Last updated: 2nd Feb 2023 at 15:12

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