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

Installation

You must install Sequana first:

pip install sequana

Then, just install this package:

pip install sequana_laa

Usage

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.

Requirements

This pipelines requires the following executable(s):

• vt
• freebayes
• igvtools
• sequana
• snpeff (optional)
• samtools
• bamtools
• minimap2

Details

This pipeline runs amplicon analysis on long reads data from pacbio sequencers.

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
0.10.0	full integration with latest wrapeprs and apptainers from damona
0.9.0	add singularity containers
0.8.0	First release.