This is is the revcomp pipeline from the Sequana projet
- Overview:
Simply reverse complement a bunch of fastq files
- Input:
fastq files
- Output:
their reverse complement counterpart
- 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
You must install Sequana first:
pip install sequana
Then, just install this package:
pip install sequana_revcomp
Usage
sequana_pipelines_revcomp --help sequana_pipelines_revcomp --input-directory DATAPATH
This creates a directory with the pipeline and configuration file. You will then need to execute the pipeline:
cd revcomp sh revcomp.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 revcomp.rules -c config.yaml --cores 4 --stats stats.txt
Or use sequanix interface.
Requirements
This pipelines requires the following executable(s):
seqtk
Details
This pipeline runs seqtk in parallel on the input fastq files.
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.
1 maintainer
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Source Distribution
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