sequana-ribofinder 0.11.0

Installation

You must install Sequana first (use –upgrade to get the latest version installed):

pip install sequana --upgrade

Then, just install this package:

pip install sequana_ribofinder --upgrade

Usage

This pipeline scans input fastq.gz files found in the local directory and identify the proportion of ribosomal content.

For help, please type:

sequana_ribofinder --help

The following command searches for input files in DATAPATH. Then, te user provide a list of rRNA sequences in FastA format in test.fasta. This command creates a directory called ribofinder/ where a snakemake pipeline can

sequana_ribofinder –input-directory DATAPATH –rRNA-file test.fasta

You will then need to execute the pipeline:

cd ribofinder
sh ribofinder.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 ribofinder.rules -c config.yaml --cores 4 --wrapper-prefix git+file:////home/user/sequana_wrappers

Or use sequanix interface.

Requirements

This pipelines requires the following executable(s):

• bowtie1

• samtools

• pigz

Details

This pipeline runs ribofinder in parallel on the input fastq files. A brief sequana summary report is also produced.

You can start from the reference file and the GFF file. By defaultm we search for the feature called rRNA:

sequana_ribofinder --input-directory . --reference-file genome.fasta --gff-file genome.gff

If the default feature rRNA is not found, no error is raised for now. If you know the expected feature, you can provide it:

sequana_ribofinder --input-directory . --reference-file genome.fasta --gff-file genome.gff --rRNA-feature gene_rRNA

If you have an existing or custom rRNA file, you can then use:

sequana_ribofinder --input-directory . --rRNA-file ribo.fasta

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