sequana-laa

JOSS (journal of open source software) DOI

https://github.com/sequana/laa/actions/workflows/main.yml/badge.svg

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

https://raw.githubusercontent.com/sequana/laa/main/sequana_pipelines/laa/dag.png

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.

Metadata

Release files for sequana-laa 0.12.0

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for sequana-laa 0.12.0
File	Size	Uploaded
sequana_laa-0.12.0.tar.gz	107.9 kB	Apr 14, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for sequana-laa 0.12.0
File	Interpreter	ABI	Platform	Reset
sequana_laa-0.12.0-py3-none-any.whl 108.3 kB Apr 14, 2026	Python 3	none	any	Details

Total release size: 216.2 kB

Release files / sequana_laa-0.12.0.tar.gz

Download URL	sequana_laa-0.12.0.tar.gz
Size	107.9 kB
Tags	Source
SHA-256 checksum How to use checksums	`959ca54a6cec9ef32cf8879dacd7cbbe67fbbfe223fb2f2b0a759ecda85e86d6`
BLAKE2b-256 checksum How to use checksums	`6722b099e28c97e580dd41f723224b92d4be6429c4ead9300c5f323a7c6e395e`
Upload date	Apr 14, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.1.0 CPython/3.13.12`

Release files / sequana_laa-0.12.0-py3-none-any.whl

Download URL	sequana_laa-0.12.0-py3-none-any.whl
Size	108.3 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`1eac5987d7aa46f30446e534d45758e6df31724bd9015e6fa2bba9f224555863`
BLAKE2b-256 checksum How to use checksums	`0cbd4e7b98246ed5be36bbbe5f63c24b3a9004601136151ec8d7ea144e2f3758`
Upload date	Apr 14, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.1.0 CPython/3.13.12`