This is is the laa pipeline from the Sequana project
| Overview: | Perform amplicon analysis on Pacbio data sets including variant and phylogeny |
|---|---|
| Input: | A set of CCS files from pacbio in FastQ formats |
| Output: | variant calling, phylogney, consensus genomes, etc |
| Status: | production but may change |
| 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 |
This pipeline was used in :
- L'Honneur et al (polyomavirus, 2022) https://pubmed.ncbi.nlm.nih.gov/34979561/
- Kali et al (rabies,2021), https://pubmed.ncbi.nlm.nih.gov/33444703/
- Claireaux et al. (gene involved in HIV, 2022) accepted, not yet on pubmed
You must install Sequana first:
pip install sequana
Then, just install this package:
pip install sequana_laa
sequana_laa --help sequana_laa --input-directory DATAPATH
This creates a directory with the pipeline and configuration file. You will then need to execute the pipeline:
cd laa sh laa.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 laa.rules -c config.yaml --cores 4 --stats stats.txt --wrapper-prefix git+file:///home/cokelaer/Work/github/forked/sequana-wrappers
Or use sequanix interface.
This pipelines requires the following executable(s):
- vt
- freebayes
- igvtools
- sequana
- snpeff (optional)
- samtools
- bamtools
- minimap2
This pipeline runs amplicon analysis on long reads data from pacbio sequencers.
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.
| Version | Description |
|---|---|
| 0.10.0 | full integration with latest wrapeprs and apptainers from damona |
| 0.9.0 | add singularity containers |
| 0.8.0 | First release. |