Quality assessment, amplicon classification and functional prediction

Workflow Type: Common Workflow Language

Workflow 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

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ID Name Description Type
forward_reads forward reads forward sequence file locally
  • File
reverse_reads reverse reads reverse sequence file locally
  • File?
forward_primer Forward primer Forward primer used
  • string
reverse_primer Reverse primer Reverse primer used
  • string?
reference_db Reference database Reference database used in FASTA format
  • string?
rev_read_len Reverse read length Read length of the reverse read
  • int?
for_read_len Reverse read length Read length of the reverse read
  • int
sample Sample name Name of the sample being analysed
  • string
fragment Subfragment name Subfragment that is being analysed (e.g. V1-V3 or V5-region)
  • string
primersRemoved Primers are removed Wether the primers are removed or not from the input files
  • boolean?
threads number of threads number of threads to use for computational processes
  • int?
metadata Metadata file UNLOCK assay metadata file
  • File?


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


ID Name Description Type
turtle n/a Used for other workflows
  • File
files_to_folder_fastqc n/a n/a
  • Directory
files_to_folder_ngtax n/a n/a
  • Directory
files_to_folder_picrust2 n/a n/a
  • Directory
files_to_folder_phyloseq n/a n/a
  • Directory

Version History

Version 2 (latest) Created 30th Sep 2021 at 12:15 by Jasper Koehorst

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Open master 6d18328

Version 1 (earliest) Created 30th Aug 2021 at 08:18 by Jasper Koehorst

Added/updated 1 files

Frozen master 8002b92
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Discussion Channel
Koehorst, J., & Nijsse, B. (2021). Quality assessment, amplicon classification and functional prediction. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.154.2

Views: 2580   Downloads: 335

Created: 30th Aug 2021 at 08:18

Last updated: 11th Oct 2021 at 13:50

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