fair_fastqc_multiqc
Perform basic QC over sequenced data
Science Score: 44.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (7.2%) to scientific vocabulary
Keywords
Repository
Perform basic QC over sequenced data
Basic Info
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 37
Topics
Metadata Files
README.md
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.
Usage
The usage of this workflow is described in the Snakemake workflow catalog it is also available locally on a single page.
Results
A complete description of the results can be found here in workflow reports.
Material and Methods
The tools used in this pipeline are described here textually.
┌──────────────────────┐
│ Copy / Link / Concat │
└──────────┬───────────┘
│
│
┌─────────────────┬──────────────┼───────────────┬────────────────┬─────────────┐
│ │ │ │ │ │
┌───▼───┐ ┌──────▼─────┐ ┌───▼──┐ ┌──────▼────┐ ┌─────▼───┐ ┌─────▼──┐
│FastQC │ │FastQ-Screen│ │SeqKit│ │fastq_utils│ │fastqinfo│ │ Seqtk │
└────┬──┘ └─────┬──────┘ └──────┘ └───────────┘ └─────────┘ └────────┘
│ │
└───┬───────────┘
┌─────▼───┐
│ MultiQC │
└─────────┘
QC
| Step | Wrapper | | ----------- | ----------------------------------------------------------------------------------------------- | | FastQC | fastqc-wrapper | | FastScreen | fastq-screen | | MultiQC | multiqc-wrapper | | SeqKit | seqkit-wrapper | | SeqTK | seqtk-wrapper | | fastq_utils | fastq_utils | | fastqinfo | fastqinfo |
Owner
- Name: tdayris
- Login: tdayris
- Kind: user
- Company: Institut Gustave Roussy
- Website: https://gustaveroussy.github.io/STRonGR/
- Repositories: 2
- Profile: https://github.com/tdayris
Bioinformatician
Citation (CITATION.cff)
authors: - family-names: Dayris given-names: Thibault orcid: https://orcid.org/0009-0009-2758-8450 cff-version: 1.2.0 date-released: '2025-06-18' message: If you use this software, please cite it as below. title: fair-fastqc-multiqc url: https://github.com/tdayris/fair_fastqc_multiqc version: 3.0.0
GitHub Events
Total
- Create event: 9
- Issues event: 2
- Release event: 9
- Issue comment event: 2
- Push event: 20
Last Year
- Create event: 9
- Issues event: 2
- Release event: 9
- Issue comment event: 2
- Push event: 20
Dependencies
- actions/checkout v3 composite
- github/super-linter v5 composite
- snakemake/snakemake-github-action v1.25.1 composite