Simulations

Generating simulations

In addition to containing a small simulated test data set (found under test/data/), the MINTIE repository also contains code for generating the simulations. The simulation code can be found under simu/. Before running, ensure that the params.ini file has its parameters correctly set. All relevant parameters can be set using this file, including the number of variants of each type to generate, reference file paths, simulation and read-generation parameters.

Note that chromosome names in the genome_fasta and gtf_ref must be in the same format. Also, we recommend using a small subsection of the genome for the gtf file (for example, chromosome 1 only). Due to pybedtools' implementation, lots of very slow iteration is required to extract certain records, and thus a full reference will take a long time to process. (We will be looking to optimise the simulation code in the future.)

Before running the simulations, please ensure ART is installed and the correct path to ART_ILLUMINA is set in the [Path] section of the parameters file.

Simulations may then be run as follows:

python run_simu.py params.ini --log simulog.txt

Logging is optional and can be used for debugging purposes only.