description: convert NGS format from one to another using bioconvert
This is is the bioconvert pipeline from the Sequana project
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
You must install Sequana first:
pip install sequana
Then, just install this package:
pip install sequana_bioconvert
You need to provide the type of conversion you wish to perform with the –command argument. You also need to tell the type of extensions expected including the compression (gz, bz2 or dsrc recognised). Finally, the –input-directory and –input-pattern must be used to find the input files.:
sequana_bioconvert --input-directory . --input-ext fastq.gz --output-ext fasta.gz --command fastq2fasta --input-pattern "*.fastq.gz"
This creates a directory with the pipeline and configuration file. You will then need to execute the pipeline:
cd bioconvert sh bioconvert.sh # for a local run
This launch a snakemake pipeline. Symboli links to the input data are created in the ./input directory and results stored in the ./output directory.
See bioconvert.readthedocs.io for more details about bioconvert itself.
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 bioconvert.rules -c config.yaml --cores 4 --stats stats.txt
Or use sequanix interface.
This pipelines requires the following executable(s):
This pipeline runs bioconvert 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.
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.