Data QC
Version 1

Workflow Type: Galaxy

Data QC step, can run alone or as part of a combined workflow for large genome assembly.

What it does: Reports statistics from sequencing reads.
Inputs: long reads (fastq.gz format), short reads (R1 and R2) (fastq.gz format).
Outputs: For long reads: a nanoplot report (the HTML report summarizes all the information). For short reads: a MultiQC report.
Tools used: Nanoplot, FastQC, MultiQC.
Input parameters: None required.
Workflow steps: Long reads are analysed by Nanoplot; Short reads (R1 and R2) are analysed by FastQC; the resulting reports are processed by MultiQC.
Options: see the tool settings options at runtime and change as required. Alternative tool option: fastp

Infrastructure_deployment_metadata: Galaxy Australia (Galaxy)

SEEK ID: https://workflowhub.eu/workflows/222?version=1

DOI: 10.48546/workflowhub.workflow.222.1

Inputs

ID	Name	Description	Type
Input file: Illumina reads R1	Input file: Illumina reads R1	n/a	File
Input file: Illumina reads R2	Input file: Illumina reads R2	n/a	File
Input file: long reads	Input file: long reads	n/a	File

ID	Name	Description
3	Nanoplot: long reads	toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1
4	FastQC on R1	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
5	FastQC on R2	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
6	MultiQC: combine fastQC reports	toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1

ID	Name	Description	Type
NanoPlot on input dataset(s): HTML report	NanoPlot on input dataset(s): HTML report	n/a	File
MultiQC on input dataset(s): Webpage	MultiQC on input dataset(s): Webpage	n/a	File