sequana-laa 0.10.0

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