This is is the fastqc pipeline from the Sequana projet
- Overview:
Runs fastqc and multiqc on a set of Sequencing data to produce control quality reports
- Input:
A set of FastQ files (paired or single-end) compressed or not
- Output:
an HTML file index.html (multiqc) and tree.html (individual fastqc report)
- Status:
production
- Citation:
Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI https://doi:10.21105/joss.00352
Installation
You must install Sequana first:
pip install sequana
Then, just install this package:
pip install sequana_fastqc
Usage
sequana_pipelines_fastqc --help sequana_pipelines_fastqc --input-directory DATAPATH
This creates a directory fastq. You just need to execute the pipeline:
cd fastqc sh fastqc.sh # for a local run
This launch a snakemake pipeline. If you are familiar with snakemake, you can retrieve the fastqc.rules and config.yaml files and then execute the pipeline yourself with specific parameters:
snakemake -s fastqc.rules --cores 4 --stats stats.txt
Or use sequanix interface.
Tutorial
You can retrieve test data from sequana_fastqc (https://github.com/sequana_fastqc) or type:
wget https://raw.githubusercontent.com/sequana/sequana_fastqc/master/sequana_pipelines/fastqc/data/data_R1_001.fastq.gz wget https://raw.githubusercontent.com/sequana/sequana_fastqc/master/sequana_pipelines/fastqc/data/data_R2_001.fastq.gz
then, prepare the pipeline:
sequana_fastqc --input-directory . cd fastqc sh fastq.sh # once done, remove temporary files (snakemake and others) make clean
Just open the HTML entry called index.html and browse the multiqc report. For individual reports, open the tree.html file. You will get expected images such as the following one:
Requirements
This pipelines requires the following executable(s):
fastqc
Details
This pipeline runs fastqc in parallel on the input fastq files (paired or not) and then execute multiqc. A brief sequana summary report is also produced.
Rules and configuration details
Here is the latest documented configuration file to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file.
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Source Distribution
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