https://github.com/sequana/depletion
Deplete Fastq files from human or other content
https://github.com/sequana/depletion
Last synced: 10 months ago
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Deplete Fastq files from human or other content
- Host: GitHub
- URL: https://github.com/sequana/depletion
- Owner: sequana
- License: bsd-3-clause
- Created: 2022-03-30T15:46:37.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2024-05-22T08:13:22.000Z (about 2 years ago)
- Last Synced: 2025-07-19T12:21:41.750Z (11 months ago)
- Language: Python
- Size: 15.3 MB
- Stars: 1
- Watchers: 2
- Forks: 2
- Open Issues: 2
-
Metadata Files:
- Readme: README.rst
- License: LICENSE
Awesome Lists containing this project
README
.. image:: https://badge.fury.io/py/sequana-depletion.svg
:target: https://pypi.python.org/pypi/sequana_depletion
.. 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
.. image:: https://github.com/sequana/depletion/actions/workflows/main.yml/badge.svg
:target: https://github.com/sequana/depletion/actions/workflows
This is is the **depletion** pipeline from the `Sequana `_ project
:Overview: select or deplete reads from input FastQ files given a reference
:Input: Fastq Files
:Output: Fastq Files
:Status: production
: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
~~~~~~~~~~~~
Install this package as follows::
pip install sequana_depletion
it requires https://sequana.readthedocs.io and https://bioconvert.readthedocs.io for the bam to fastq conversion
Usage
~~~~~
::
sequana_depletion --help
sequana_depletion --input-directory DATAPATH --reference hg38.fa --mode depletion
sequana_depletion --input-directory DATAPATH --reference covid.fa --mode selection
This creates a directory with the pipeline and configuration file. You will then need
to execute the pipeline::
cd depletion
sh depletion.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 depletion.rules -c config.yaml --cores 4 --stats stats.txt
Or use `sequanix `_ interface.
Requirements
~~~~~~~~~~~~
This pipelines requires the following executable(s):
- bwa
- samtools
- bamtools
#.. image:: https://raw.githubusercontent.com/sequana/depletion/master/sequana_pipelines/depletion/dag.png
Details
~~~~~~~~~
This pipeline runs **depletion** in parallel on the input fastq files (paired or not).
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.
Changelog
~~~~~~~~~
========= ====================================================================
Version Description
========= ====================================================================
0.3.0 * use click and new sequana_pipetools. convert to pyproject
0.2.0 * handle paired/unpaired data
* refactorise to use containers/apptainers
0.1.0 **First release.**
========= ====================================================================