BleTIES is a tool for prediction and targeted assembly of internally eliminated sequences (IESs) in ciliate genomes, using single-molecule long read sequencing. The design and name of the software was inspired by ParTIES.
The required inputs are a ciliate MAC genome assembly, and a long read sequencing library (PacBio subreads or error-corrected CCS reads, or Nanopore reads) mapped onto that assembly. The mapper should report a valid CIGAR string and NM tag (for number of mismatches) per aligned read. The mapping is assumed to be accurate.
Read more in our paper.
The released versions are distributed via Bioconda, and can be installed with Conda:
# Create new environment called "bleties"
conda create -c conda-forge -c bioconda -n bleties bleties
# Activate environment
conda activate bleties
# Check version and view help message
bleties --version
bleties --help
# Run tests
python -m unittest -v bleties.TestModuleIf you want to test the latest development version, clone this Git repository, then install with pip.
Dependencies are specified as a Conda environment YAML file env.yaml. Create a
Conda environment with the specified dependencies, then install with pip:
git clone git@github.com:Swart-lab/bleties.git
cd bleties
conda env create -f env.yaml -n bleties_dev
conda activate bleties_dev
pip install .Run tests after installation:
python -m unittest -v bleties.TestModuleFor help, use the -h or --help option, with or without the subworkflow
names:
bleties --help
bleties milraa --help
bleties miser --help
bleties milret --help
bleties milcor --help
bleties miltel --help
bleties insert --help
The main module for IES reconstruction is MILRAA. At the moment, it only handles non-scrambled IESs.
Two scripts are available for plotting visualizations of MILRAA and MILCOR
results: milcor_plot.py and milraa_plot.py.
Additional useful scripts are in the folder scripts/
Refer to the full documentation for more information.
BleTIES is research software. Please cite us if you use the software in a publication.