MitoIMP: A computational framework for imputation of missing data in low-coverage human mitochondrial genome
・python 2.7 (pypy2)
・MAFFT: Multiple alignment program for amino acid or nucleotide sequences
Please refer to the official site for details of the installation of MAFFT.
Clone this repository into your local machine
git clone https://github.com/omics-tools/mitoimp.git
Basic Usage
mitoimp.py -i input.fasta [-k 5] [-f 0.7] [-t 4]
Example1
An imputed sequence and a summary table are output to the same directory as the input file.
mitoimp.py -i ./sample_data/A_cov65.fasta -k 5 -f 0.7 -t 4
Example2
If you want to use a sequence oriented to the rCRS position by other alignment software, please set -no_aln flag.
mitoimp.py -i ./sample_data/Z_cov85.fasta -k 5 -f 0.7 -t 4 -no_aln
optional arguments:
| Flag | Description | File Format, Parameter etc. |
|---|---|---|
| -i | query sequence (required) | Single-FASTA format |
| -p | in-house (customized) panel sequences | Multi-FASTA format |
| -w | window-size (default: 16569) | 1 〜 16569 |
| -k | k-number (default: 5) | 1 〜 max of panel sequences |
| -f | the threshold frequency to determine a genotype (default: 0.7) | 0.5 〜 1.0 |
| -t | multiprocessing numbers (default: the max of available CPU-threads) | 1 〜 (max: -1) |
| -no_aln | set a switch to non-alignment mode (default: Disable) | |
| -v | show program's version number and exit | |
| -h | show this help message and exit |
1.0.1 (beta)
[MIT] https://github.com/omics-tools/mitoimp/blob/master/LICENSE
Ishiya, K., Mizuno, F., Wang, L., & Ueda, S. (2019). MitoIMP: A Computational Framework for Imputation of Missing Data in Low-Coverage Human Mitochondrial Genome. Bioinformatics and biology insights.