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.. image:: http://joss.theoj.org/papers/10.21105/joss.00352/status.svg :target: http://joss.theoj.org/papers/10.21105/joss.00352 :alt: JOSS (journal of open source software) DOI

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This is is the downsampling pipeline from the Sequana <https://sequana.readthedocs.org>_ project

:Overview: downsample NGS data sets :Input: a set of FastQ or FASTA files :Output: a set of downsampled files :Status: production :Citation(sequana): 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 :Citation(pipeline): .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4047837.svg :target: https://doi.org/10.5281/zenodo.4047837

Installation

You must install Sequana first::

    pip install sequana

Then, just install this package::

    pip install sequana_downsampling

Usage

::

sequana_downsampling --help
sequana_downsampling --input-directory DATAPATHH
sequana_downsampling --downsampling-method random --downsampling-max-entries 100
sequana_downsampling --downsampling-method random_pct --downsampling-percent 10 --downsampling-input-format fasta --input-pattern "whatever*fasta"

Note that the current implementation handles fastq files (zipped or not) and fasta files (uncompressed only)

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 <https://sequana.readthedocs.io/en/master/sequanix.html>_ interface.

Examples of a set of FastQ zipped files in the current directory:

sequana_downsampling --run --downsampling-method random_pct 
cd downsampling
make clean

This will create a directory called downsampling, and randomly select 10% of the input reads for each file with extension .fastq.gz in the current directory. Since -run is used, the pipeline is executed automatically. The following commands will enter into the directory and called a Makefile. This will clean the directory for temporary files.

Requirements

This pipelines requires the following executable(s):

- sequana
- pigz

.. .. image:: https://raw.githubusercontent.com/sequana/downsampling/master/sequana_pipelines/downsampling/dag.png

Details

This pipeline runs downsampling in parallel on the input fastq or fasta files (paired or not). If paired, the one-to-one mapping is conserved.

It can take as input a set of FastQ files, or FastA files. by default, the pipeline with randomly select 1000 entries from each input files. You can increase this number using --downsampling-max-entries option. If you prefer to select a percentage of the entries instead, you can change the downsamping method as follows::

--downsampling-method random_pct

and change the value if needed (default is 10%)::

--downsampling-percent 20

Note that input FastQ can be gzipped. Output files are gzipped. FastA input files must be compressed for now

Rules and configuration details

Here is the `latest documented configuration file <https://raw.githubusercontent.com/sequana/downsampling/master/sequana_pipelines/downsampling/config.yaml>`_
to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file. 

Changelog

========= ==================================================================== Version Description ========= ==================================================================== 0.8.5 cope with R1/R2 paired data properly. Improved make file 0.8.4 add missing MANIFEST to include missing requirements.txt 0.8.3 comply with new API from sequana_pipetools 0.2.4 0.8.2 add a --run option to execute the pipeline directly 0.8.1 * fix input and N in the random selection 0.8.0 First release. ========= ====================================================================