A simple mapper to map reads onto a reference. This is useful for quick QCs and also secondary analysis
This is is the mapper pipeline from the Sequana projet
|Overview:||This is a simple pipeline to map several FastQ files onto a reference using different mappers/aligners|
|Input:||A set of FastQ files.|
|Output:||A set of BAM files|
|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|
You must install Sequana first:
pip install sequana
Then, just install this package:
pip install sequana_mapper
sequana_pipelines_mapper --help sequana_pipelines_mapper --input-directory DATAPATH
This creates a directory with the pipeline and configuration file. You will then need to execute the pipeline:
cd mapper sh mapper.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 mapper.rules -c config.yaml --cores 4 --stats stats.txt
Or use sequanix interface.
This pipelines requires the following executable(s):
This pipeline runs mapper 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.
|Filename, size||File type||Python version||Upload date||Hashes|
|Filename, size sequana_mapper-0.8.2.tar.gz (273.9 kB)||File type Source||Python version None||Upload date||Hashes View hashes|