Quality assessment, amplicon classification and functional prediction
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Download RO-CrateWorkflow for quality assessment of paired reads and classification using NGTax 2.0 and functional annotation using picrust2.
In addition files are exported to their respective subfolders for easier data management in a later stage.
Steps:
- FastQC (read quality control)
- NGTax 2.0
- Picrust 2
- Export module for ngtax
Click and drag the diagram to pan, double click or use the controls to zoom.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| forward_reads | forward reads | forward sequence file locally |
|
| reverse_reads | reverse reads | reverse sequence file locally |
|
| forward_primer | Forward primer | Forward primer used |
|
| reverse_primer | Reverse primer | Reverse primer used |
|
| reference_db | Reference database | Reference database used in FASTA format |
|
| rev_read_len | Reverse read length | Read length of the reverse read |
|
| for_read_len | Reverse read length | Read length of the reverse read |
|
| sample | Sample name | Name of the sample being analysed |
|
| fragment | Subfragment name | Subfragment that is being analysed (e.g. V1-V3 or V5-region) |
|
| primersRemoved | Primers are removed | Wether the primers are removed or not from the input files |
|
| threads | number of threads | number of threads to use for computational processes |
|
| metadata | Metadata file | UNLOCK assay metadata file |
|
Steps
| ID | Name | Description |
|---|---|---|
| fastqc | n/a | n/a |
| reads_to_folder | n/a | n/a |
| ngtax | n/a | n/a |
| ngtax_to_tsv-fasta | n/a | n/a |
| picrust2 | n/a | n/a |
| folder_compression | n/a | n/a |
| fastqc_files_to_folder | n/a | n/a |
| ngtax_files_to_folder | n/a | n/a |
| picrust_files_to_folder | n/a | n/a |
| phyloseq_files_to_folder | n/a | n/a |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| turtle | n/a | Used for other workflows |
|
| files_to_folder_fastqc | n/a | n/a |
|
| files_to_folder_ngtax | n/a | n/a |
|
| files_to_folder_picrust2 | n/a | n/a |
|
| files_to_folder_phyloseq | n/a | n/a |
|
Version History
Version 2 (latest) Created 30th Sep 2021 at 12:15 by Jasper Koehorst
Open
master6d18328
Version 1 (earliest) Created 30th Aug 2021 at 08:18 by Jasper Koehorst
Added/updated 1 files
Frozen
master
8002b92
Creators and Submitter
Views: 3118 Downloads: 481
Created: 30th Aug 2021 at 08:18
Last updated: 11th Oct 2021 at 13:50
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