MGnify's amplicon pipeline v5.0 - Quality control SE

Quality control subworkflow for single-end reads.

Associated Tutorial

This workflows is part of the tutorial MGnify v5.0 Amplicon Pipeline, available in the GTN

Workflow Author(s): MGnify - EMBL, Rand Zoabi, Paul Zierep

Tutorial Author(s): Rand Zoabi

Tutorial Contributor(s): Paul Zierep, Saskia Hiltemann

Funder(s): German Competence Center Cloud Technologies for Data Management and Processing (de.KCD)

Inputs

ID	Name	Description	Type
Ambiguity filtering - Maximal N percentage threshold to conserve sequences	#main/Ambiguity filtering - Maximal N percentage threshold to conserve sequences	Maximal N percentage threshold to conserve sequences.	int
Length filtering - Minimum size	#main/Length filtering - Minimum size	Minimum sequence length.	int
Single-end reads	#main/Single-end reads	Single-end reads collection.	array containing File
Trimmomatic - LEADING	#main/Trimmomatic - LEADING	Cut bases off the start of a read, if below a threshold quality.	int
Trimmomatic - MINLEN	#main/Trimmomatic - MINLEN	Minimum length of reads to be kept.	int
Trimmomatic - SLIDING WINDOW - Average quality required	#main/Trimmomatic - SLIDING WINDOW - Average quality required	Average quality required.	int
Trimmomatic - SLIDING WINDOW - Number of bases to average across	#main/Trimmomatic - SLIDING WINDOW - Number of bases to average across	Number of bases to average across.	int
Trimmomatic - TRAILING	#main/Trimmomatic - TRAILING	Cut bases off the end of a read, if below a threshold quality.	int

Steps

ID	Name	Description
8	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1
9	Trimming	toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.39+galaxy2
10	Replace	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0
11	Length filtering	toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5+galaxy2
12	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1
13	Ambiguity filtering	toolshed.g2.bx.psu.edu/repos/iuc/prinseq/prinseq/0.20.4+galaxy2
14	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1
15	Replace	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0
16	FASTQ to FASTA	toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.5+galaxy2
17	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1
18	Replace	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0
19	FASTA Width	toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2
20	Replace	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0
21	MultiQC	toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3

Outputs

ID	Name	Description	Type
Single-end MultiQC report	#main/Single-end MultiQC report	n/a	File
Single-end MultiQC statistics	#main/Single-end MultiQC statistics	n/a	File
Single-end post quality control FASTA files	#main/Single-end post quality control FASTA files	n/a	File