Snakemake workflow used to control read qualities over fastq files with FastQC.
This pipeline is meant to be used in teaching sessions or imported in other snakemake-workflows.
The usage of this workflow is described in the Snakemake workflow catalog it is also available locally on a single page.
A complete description of the results can be found here in workflow reports.
The tools used in this pipeline are described here textually.
┌──────────────────────┐
│ Copy / Link / Concat │
└──────────┬───────────┘
│
│
┌─────────────────┬──────────────┼───────────────┬────────────────┐
│ │ │ │ │
┌───▼───┐ ┌──────▼─────┐ ┌───▼──┐ ┌──────▼────┐ ┌─────▼──┐
│FastQC │ │FastQ-Screen│ │SeqKit│ │fastq_utils│ │fastinfo│
└────┬──┘ └─────┬──────┘ └──────┘ └───────────┘ └────────┘
│ │
└───┬───────────┘
┌─────▼───┐
│ MultiQC │
└─────────┘
| Step | Wrapper |
|---|---|
| FastQC | fastqc-wrapper |
| FastScreen | fastq-screen |
| MultiQC | multiqc-wrapper |
| SeqKit | seqkit-wrapper |
| fastq_utils | fastq_utils |
| fastqinfo | fastqinfo |