Quality assessment, amplicon classification and functional prediction
Version 1

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

Inputs

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?

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
  • 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
Total size: 31.5 MB
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Views: 109

Created: 30th Sep 2021 at 13:16

Last used: 26th Nov 2021 at 19:07

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Version History

master @ ba86bfb (earliest) Created 30th Sep 2021 at 13:16 by Finn Bacall

metadata added and picrust under an optional condition when 0 asvs are found


Frozen master ba86bfb

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