taxonomy, sequana, kraken, snakemake
Project description
This is is the multitax pipeline from the Sequana project
- Overview:
Runs taxonomic analysis on a set of samples using sequana_taxonomy (kraken behing the scene)
- Input:
A set of Fastq files
- Output:
HTML report for each sample and a summary HTML report for all (multiqc + dendogram)
- 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_multitax
Usage
sequana_pipelines_multitax --help sequana_pipelines_multitax --input-directory DATAPATH --databases toydb
For the database, you will need to provide your own databases. You can check out the documentation of kraken. The toydb here above is shipped wit sequana and should work for demo. See sequana_taxonomy standalone for more help and information. You can also checkout the sequana documentation (kraken module)
This creates a directory with the pipeline and configuration file. You will then need to execute the pipeline:
cd multitax sh multitax.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 multitax.rules -c config.yaml --cores 4 --stats stats.txt
Or use sequanix interface.
Requirements
This pipelines requires the following executable(s):
kraken
kraken2
sequana_taxonomy
Details
This pipeline runs sequana_taxonomy (based on kraken) 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 |
---|---|
0.8.0 |
First release. |
Project details
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