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)
|Input file: Illumina reads R1||Input file: Illumina reads R1||n/a||
|Input file: Illumina reads R2||Input file: Illumina reads R2||n/a||
|Input file: long reads||Input file: long reads||n/a||
|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|
|NanoPlot on input dataset(s): HTML report||NanoPlot on input dataset(s): HTML report||n/a||
|MultiQC on input dataset(s): Webpage||MultiQC on input dataset(s): Webpage||n/a||
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Created: 8th Nov 2021 at 04:34
Last updated: 9th Nov 2021 at 01:09