sequana-laa 0.12.0

Long read amplicon analysis

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) https://pubmed.ncbi.nlm.nih.gov/35082297/

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
bash laa.sh  # for a local run

This launches a snakemake pipeline.

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
0.12.0	migrated to modern sequana layout (poetry, rich_click, no click_completion); wrapper: directives replaced by manager.get_shell shells or inline shell/run blocks; dedicated igvtools apptainer; samtools faidx rule to build the reference index
0.11.0	add apptainer containers
0.10.0	full integration with latest wrapeprs and apptainers from damona
0.9.0	add singularity containers
0.8.0	First release.