This is the trf (tandem repeat finder) pipeline from the Sequana project

Overview:	run TRF on several large datasets
Input:	a set of FastA files
Output:	TRF output + images
Status:	draft
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

Installation

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

pip install sequana_trf --upgrade

Otherwise, you can create a sequana_trf conda environment executing:

conda env create -f environment.yml

and later activate the environment:

conda activate sequana_trf

A third option is to install the pipeline with pip method (see above) and use singularity as explained afterwards.

Usage

sequana_trf --help
sequana_trf --input-directory DATAPATH

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

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

Or use sequanix interface.

Requirements

This pipeline requires the following executable(s):

• trf

Details

This pipeline runs trf in parallel on the input fastq files (paired or not). A brief sequana summary report is also produced.

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
1.0.0	Uses click and pyproject
0.10.0	update and add singularity containers
0.9.3	Use new sequana / sequana_pipetools API
0.9.2	Better split function of input fasta file
0.9.0	First release.