Longread 16S classification workflow Version 1
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Download RO-CrateWorkflow 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
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 |
|
| reads | Read file | Read file in FASTA or FASTQ format (can be gz) |
|
| reference_db | Reference database | Reference database used in FASTA format |
|
| readtype | Read type | Type of read nanopore or pacbio. default nanopore |
|
| 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) |
|
| threads | Number of threads | Number of threads to use for computational processes |
|
| skip_read_filter | Skip quality filtering | Skip quality reporting and filtering. (Default false) |
|
| 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)" |
|
| qualified_quality_phred | Qualified_quality_phred | the quality value that a base is qualified. Default 8 means phred quality >=Q9 is qualified. |
|
| mean_qual | Mean quality | if one read's mean_qual quality score < mean_qual, then this read is discarded. (Default 10) |
|
| minimum_length | Minimum length required | Reads shorter will be discarded. (Default 1200) |
|
| length_limit | Maximum length limit | Reads longer than length_limit will be discarded. (Default 1600) |
|
| trim_front | Trim_front | Trimming how many bases in front for read. (Default not set, 0) |
|
| trim_tail | trim_tail | Trimming how many bases in tail for read. (Default not set, 0) |
|
| 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 |
|
| 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. |
|
| cut_window_size | Cut window size | The window size option shared by cut_front, cut_tail or cut_sliding. Range: 1~1000. Default 4 |
|
| 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 |
|
| start_adapter | start_adapter | The adapter sequence at read start (5'). (Default auto-detect) |
|
| end_adapter | End adapter | The adapter sequence at read end (3'). (Default auto-detect) |
|
| adapter_fasta | Adapter fasta | Specify a FASTA file to trim both read ends by all the sequences in this FASTA file. (Default None) |
|
| disable_adapter_trimming | Disable adapter trimming | Adapter trimming is enabled by default. If this option is specified, adapter trimming is disabled. Default true |
|
| output_filtered_reads | Output filtered reads | Output filtered reads when filtering is applied. (Default false) |
|
| destination | Output Destination | Optional Output destination used for cwl-prov reporting. |
|
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 |
|
| filtered_reads | n/a | Filtered reads output file |
|
| emu_abundance | Emu abundances | n/a |
|
| emu_read_assignment_distributions | Emu read assignment distribution | n/a |
|
| emu_unclassified | Emu unclassified | n/a |
|
Version History
Version 1 (earliest) Created 10th Sep 2025 at 13:31 by Bart Nijsse
Initial commit
Open
masterd20af19
Creators and Submitter
Views: 42 Downloads: 7
Created: 10th Sep 2025 at 13:30
Last updated: 10th Sep 2025 at 14:40
AttributionsNone
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