Given some FASTA files, will simulate FASTQs from them using ART, and then mix them together in the desired proportions. Should work on any UNIX-based system.
- The ART executable (art_illumina) must be on your $PATH.
- biopython >= 1.70
- OLCTools >= 0.3.45
To install both, use pip: pip install biopython olctools
Clone this repository - you'll want to use the simulate_and_mix.py script.
usage: simulate_and_mix.py [-h] -bf BASE_FASTA -cf CONTAMINANT_FASTA
[-d DEPTH] [-t TMPDIR] -fc FRACTION_CONTAMINATION
[-o OUTPUT_DIRECTORY]
optional arguments:
-h, --help show this help message and exit
-bf BASE_FASTA, --base_fasta BASE_FASTA
Path to fasta-formatted file for base genome.
-cf CONTAMINANT_FASTA, --contaminant_fasta CONTAMINANT_FASTA
Path to fasta-formatted file for base genome.
-d DEPTH, --depth DEPTH
Coverage depth desired for output genome. Defaults to
60X.
-t TMPDIR, --tmpdir TMPDIR
Temporary directory name.
-fc FRACTION_CONTAMINATION, --fraction_contamination FRACTION_CONTAMINATION
Contamination fraction. Must be between 0 and 1.
-o OUTPUT_DIRECTORY, --output_directory OUTPUT_DIRECTORY
Output directory for your FASTQ files. Defaults to
current working directory.