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

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?

Steps

ID Name Description
fastqc
reads_to_folder
ngtax
ngtax_to_tsv-fasta
picrust2
fastqc_files_to_folder
ngtax_files_to_folder
picrust_files_to_folder
phyloseq_files_to_folder

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
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Views: 107   Downloads: 1

Created: 30th Aug 2021 at 08:18

Last used: 26th Sep 2021 at 07:44

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Version History

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

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