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 |
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
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.
This pipelines requires the following executable(s):
- bwa
- bioconvert
- samtools
- bamtools
#.. image:: https://raw.githubusercontent.com/sequana/depletion/master/sequana_pipelines/depletion/dag.png
This pipeline runs depletion in parallel on the input fastq files (paired or not). A brief sequana summary report is also produced.
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.
| Version | Description |
|---|---|
| 0.1.0 | First release. |