Crusty-Neat Project

A diverging fork of the rusty_neat project, designed to simulate genomic mutations and generate sequencing reads based on a reference genome. In this version, a significant portion of the original code has been rewritten to optimize performance and shared-memory parallelism, adopting libraries like DashMap and Rayon for improved efficiency.

🚧 Work in Progress: This project is actively being developed, and changes are ongoing.

How to run

Clone the repository and run the software with:

cargo run -r -- -c config/crusty_test.yml --log-level debug

In this example:

• The -c flag specifies the path to the configuration file (config/crusty_test.yml).
• The --log-level debug flag sets the logging level to debug.

Configuration file:

The configuration file defines the parameters for the software. The values can be modified in the file, or you can override them directly from the command line. Below is an example of a configuration file:

reference: test_data/ecoli.fa
read_len: 150
coverage: 5

def_mutation_rate: 0.001
mutation_model: models/mut_model.yml
quality_model: models/quality_model.yml.gz
rng_seed: null

ploidy: 2
paired_ended: true
fragment_mean: 300.0
fragment_st_dev: 30.0

produce_fastq: true
produce_bam: false
produce_vcf: true
produce_fasta: true

overwrite_output: true
output_dir: /tmp/test_output
output_prefix: ecoli

Overriding Configuration Values

Values defined in the configuration file can be overridden by passing the corresponding flags directly from the command line. For example:

cargo run -r -- -c config/crusty_test.yml --log-level debug --read_len 100 --coverage 10

For a full list of command line parameters just run

cargo run -r -- -h

License

This project is licensed under the BSD-3-Clause license.

Authors

The original rusty_neat has been developed by the NEAT Contributors.

Crusty-Neat is being developed by:

• Francesco Versaci, CRS4 francesco.versaci@crs4.it