This is is the downsampling pipeline from the Sequana project
- Overview:
downsample NGS data sets
- Input:
a set of FastQ or FASTA files
- Output:
a set of downsampled files
- Status:
mature
- Citation:
Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI doi:10.21105/joss.00352
Installation
You must install Sequana first:
pip install sequana
Then, just install this package:
pip install sequana_downsampling
Usage
sequana_pipelines_downsampling --help sequana_pipelines_downsampling --input-directory DATAPATHH sequana_downsampling --downsampling-method random --downsampling-max-entries 100
This creates a directory with the pipeline and configuration file. You will then need to execute the pipeline:
cd downsampling sh downsampling.sh # for a local run
This launch a snakemake pipeline. If you are familiar with snakemake, you can retrieve the pipeline itself and its configuration files and then execute the pipeline yourself with specific parameters:
snakemake -s downsampling.rules -c config.yaml --cores 4 --stats stats.txt
Or use sequanix interface.
Requirements
This pipelines requires the following executable(s):
sequana
pigz
Details
This pipeline runs downsampling in parallel on the input fastq or fasta files (paired or not).
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.
Changelog
Version |
Description |
|---|---|
0.8.3 |
|
0.8.2 |
|
0.8.1 |
|
0.8.0 |
First release. |
1 maintainer
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Source Distribution
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