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
- Status:
draft
- 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
You must install Sequana first:
pip install sequana
Then, just install this package:
pip install sequana_mapper
Usage
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.
Requirements
This pipelines requires the following executable(s):
bamtools
bwa
multiqc
sequana_coverage
minimap2
Details
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.
Changelog
Version |
Description |
|---|---|
0.8.4 |
|
0.8.3 |
|
0.8.2 |
|
0.8.1 |
|
0.8.0 |
First release. |
1 maintainer
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