README.md

NIPT-PG

NIPT-PG: Empowering Non-Invasive Prenatal Testing to learn from population genomics through an incremental pan-genomic approach

Step 1. Package Dependency

first, install the NIPT-PG conda environment:

conda create -c NIPT-PG

conda activate NIPT-PG

then, in NPIT-PG environment, install the following package:

pip install pandas numpy tqdm argparse

Step 2. generating pan-genome

usage:

python3 gen_pgg.py [-r REF.FA_FILE] [-s SAM_PATH] [-n NIPT_FILE]

optional arguments:

• -r path to the reference genome file (such as GRCh38.fa)

• -s path to the folder containing the files to be tested

• -n path to the nipt_files.csv

example:

python3 gen_pgg.py -r data/ref.fa -s data/sam/ -n data/nipt_files_ART-Random.csv

The content of the nipt_files.csv file is as illustrated in Table 1, documenting the file name mappings for each testing file. This practice aids in standardizing file management and enhances testing efficiency.

Table 1. Illustration of the nipt_files.csv file.

id	nipt_files	mapping
0	CL100050702_L02_91	sample_0
1	CL100025607_L02_22	sample_1
2	CL100035831_L01_15	sample_2
...	...	...

Step 3. Sequence-to-graph alignment

usage:

python3 map2pgg.py [-p PGG_FILE] [-s SAM_PATH] [-n NIPT_FILE] [-k K_MER]

optional arguments:

• -p the pan-genome file path

• -s path to the folder containing the files to be tested

• -n path to the nipt_files.csv

• -k k-mer length, default=5

example:

python3 map2pgg.py -p data/pgg.json -s data/sam/ -n data/nipt_files_ART-Random.csv -k 5

Step 4. Z-score test based on multi-source aligned read

usage:

python3 aneup_det.py [-s SAM_PATH] [-g ALIGNED_SAM_PATH] [-n NIPT_FILE] 
[-l LEFT_THRESHOLD] 
[-r RIGHT_THRESHOLD]
[-c CONTROL SAMPLE]

optional arguments:

• -s path to the folder containing the files to be tested

• -g path to the folder containing realigned samples

• -n path to the nipt_files.csv

• -l left threshold of z-score (default = -3)

• -r right threshold of z-score (default = 3)

example:

python3 aneup_det.py -s data/sam/ -g data/aligned_sam/ -n data/nipt_files_ART-Random.csv -l -3 -r 3