git clone https://github.com/pratas/amito.git
cd amitoOn Ubuntu/Debian:
sudo apt update
sudo apt install -y ncbi-blast+ samtools python3 python3-pip
python3 -m pip install --user numpy pandas matplotlibchmod +x *.sh
./download_and_extract_numts_T2T.shThis step downloads or processes the references, searches the human nuclear genome for NUMTs, filters the alignments and extracts the candidate regions.
python3 plot_numts.py human_NUMTs_coordinates.tsv
python3 plot_numt_substitution_spectrum.py human_NUMTs_substitution_spectrum.tsvpython3 paracoccus_substitution_spectrum.py human_mitogenome.fasta paracoccus_denitrificans_genome.fastaTHREADS=8 READS_PER_GROUP=50000 READ_LENGTHS=25,30,35,50,75 FORCE=1 ./run_competitive_mapping_benchmark.shThis project is licensed under the GNU General Public License v3.0 (GPLv3).
See the LICENSE file for the complete license text.