Longread Amplicon workflow

Workflow for quality assessment and taxonomic classification of amplicon long read sequences.
In addition files are exported to their respective subfolders for easier data management in a later stage.

Inputs are expected to be basecalled fastq files

Steps:
- NanoPlot read quality control, before and after filtering
- fastplong read quality and length filtering
- Emu abundance; species-level taxonomic abundance for full-length 16S read

Inputs

ID	Name	Description	Type
identifier	identifier used	Identifier for this dataset used in this workflow	string
reads	Read file	Read file in FASTA or FASTQ format (can be gz)	File[]
reference_db	Reference database	Reference database used in FASTA format	Directory
readtype	Read type	Type of read nanopore or pacbio. default nanopore	<strong>enum</strong> of: nanopore, pacbio
fastq_rich	Fastq rich (ONT)	Input fastq is generated by albacore, MinKNOW or guppy with additional information concerning channel and time. Used to creating more informative quality plots (default false)	boolean
threads	Number of threads	Number of threads to use for computational processes	int?
skip_read_filter	Skip quality filtering	Skip quality reporting and filtering. (Default false)	boolean
disable_quality_filtering	Disable_quality_filtering	"Quality filtering is enabled by default. If this option is specified, quality filtering is disabled. Quality plots will still be generated when skip_read_filter is false. (Default false)"	boolean?
qualified_quality_phred	Qualified_quality_phred	the quality value that a base is qualified. Default 8 means phred quality >=Q9 is qualified.	int?
mean_qual	Mean quality	if one read's mean_qual quality score < mean_qual, then this read is discarded. (Default 10)	int?
minimum_length	Minimum length required	Reads shorter will be discarded. (Default 1200)	int?
length_limit	Maximum length limit	Reads longer than length_limit will be discarded. (Default 1600)	int?
trim_front	Trim_front	Trimming how many bases in front for read. (Default not set, 0)	int?
trim_tail	trim_tail	Trimming how many bases in tail for read. (Default not set, 0)	int?
cut_front	Cut front	Move a sliding window from front (5') to tail, drop the bases in the window if its mean quality < threshold, stop otherwise. Default false	boolean?
cut_tail	Cut tail	Move a sliding window from tail (3') to front, drop the bases in the window if its mean quality < threshold, stop otherwise Default false.	boolean?
cut_window_size	Cut window size	The window size option shared by cut_front, cut_tail or cut_sliding. Range: 1~1000. Default 4	int?
cut_mean_quality	Cut mean quality	The mean quality requirement option shared by cut_front, cut_tail or cut_sliding. Range: 1~36. Default 20	int?
start_adapter	start_adapter	The adapter sequence at read start (5'). (Default auto-detect)	string?
end_adapter	End adapter	The adapter sequence at read end (3'). (Default auto-detect)	string?
adapter_fasta	Adapter fasta	Specify a FASTA file to trim both read ends by all the sequences in this FASTA file. (Default None)	File?
disable_adapter_trimming	Disable adapter trimming	Adapter trimming is enabled by default. If this option is specified, adapter trimming is disabled. Default true	boolean
output_filtered_reads	Output filtered reads	Output filtered reads when filtering is applied. (Default false)	boolean
destination	Output Destination	Optional Output destination used for cwl-prov reporting.	string?

Steps

ID	Name	Description
workflow_merge_reads	Merge paired reads	Creates a single file object. Also merges reads if multiple files are given.
workflow_longread_quality	Oxford Nanopore quality workflow	Quality, filtering and taxonomic classification workflow for Oxford Nanopore reads
emu	Emu abundance	Emu abundance; species-level taxonomic abundance for full-length 16S read
step_output_filtered_reads	Output reads	Step needed to output filtered reads.

Outputs

ID	Name	Description	Type
quality_folder	NanoPlot	Folder with quality plots from Nanoplot	Directory?
filtered_reads	n/a	Filtered reads output file	File?
emu_abundance	Emu abundances	n/a	File
emu_read_assignment_distributions	Emu read assignment distribution	n/a	File
emu_unclassified	Emu unclassified	n/a	File

Longread Amplicon workflow
Version 1

Inputs

Steps

Outputs

Version History

Version 1 (earliest) Created 10th Sep 2025 at 13:31 by Bart Nijsse

Creators

Submitter

Longread Amplicon workflow Version 1

Inputs

Steps

Outputs

Version History

Version 1 (earliest) Created 10th Sep 2025 at 13:31 by Bart Nijsse

Creators

Submitter

Related items

Longread Amplicon workflow
Version 1