sequana-multitax 0.12.1

Installation

If you already have all requirements, you can install the packages using pip:

pip install sequana_multitax --upgrade

Usage

In order to use this pipeline, you will need Kraken databases. Please see Kraken pages for help.

We will also need a taxonomic databases. In principle this pipeline will download the file in your home, in /home/user/.config/sequana/taxonomy.dat one for all. Note, that with singularity, this file will be downloaded locally in your working directory for each analysis,except if it is found in your home, in which case a simple copy is performed.

sequana_multitax --help
sequana_multitax --input-directory DATAPATH  --databases toydb

For the database, you will need to provide your own databases. You can check out the documentation of kraken. The toydb here above is shipped with sequana and should work for demo. See sequana_taxonomy standalone for more help and information. You can also checkout the sequana documentation (kraken module).

The Kraken final report and blast analysis (if set) will need a taxonomic file stored in the sequana config directory (HOME/.config/sequana/taxonomy.dat). If not already done, type this command:

sequana_multitax --update-taxonomy

You may need to call this command from time to time if unknown taxon appears in the HTML reports.

This creates a directory with the pipeline and configuration file. You will then need to execute the pipeline:

cd multitax
sh multitax.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 multitax.rules -c config.yaml --cores 4 --stats stats.txt

Or use sequanix interface.

Usage with singularity::

With singularity, initiate the working directory as follows:

sequana_multitax --use-singularity ...

Images are downloaded in the working directory but you can store then in a directory globally (e.g.):

sequana_multitax --use-singularity --singularity-prefix ~/.sequana/apptainers

and then:

cd multitax
sh multitax.sh

if you decide to use snakemake manually, do not forget to add singularity options:

snakemake -s multitax.rules -c config.yaml --cores 4 --stats stats.txt --use-singularity --singularity-prefix ~/.sequana/apptainers --singularity-args "-B /home:/home"

Requirements

This pipelines requires the following executable(s):

• kraken2

• sequana_taxonomy

• krona

You can download databases from kraken website. We provide some databases on https://github.com/sequana/resources. You can download a toy database as follows:

sequana_taxonomy --download toydb

The first time, a taxonomic database will be downloaded and stored locally in .config/sequana/taxonomy.dat file. You can update it from time to time using:

sequana_taxonomy --update-taxonomy

Details

This pipeline runs sequana_taxonomy (based on kraken) in parallel on the input fastq files (paired or not). A brief sequana summary report is also produced. For each sample, a HTML page is reported with the following kind of image. This pie chart is a static image summarizing the species found in your sample. Unclassified reads are in grey. Colors correspond to a kingdom (green for viruses). If you click on the image, you will be redirect to a more precise pie chart base on Krona pie chart, which is more interactive.

The analysis is enterily based on Kraken tool. If several databases are provided, they are run sequentially. This requires a careful interpretation of the results. Indeed analysing data with viruses then bacteria may give different results as compare to analysing with bacteria then viruses.

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