https://github.com/haradama/plasmidpicker
Software to identify plasmid sequence data from metagenome using logistic regression and Minhash
https://github.com/haradama/plasmidpicker
bioinformatics classification contigs fasta logistic-regression metagenome metagenomics minhash plasmids
Last synced: about 2 months ago
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Software to identify plasmid sequence data from metagenome using logistic regression and Minhash
- Host: GitHub
- URL: https://github.com/haradama/plasmidpicker
- Owner: haradama
- License: mit
- Created: 2018-07-03T06:31:25.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2018-11-19T10:38:40.000Z (over 6 years ago)
- Last Synced: 2025-04-13T20:48:20.615Z (about 2 months ago)
- Topics: bioinformatics, classification, contigs, fasta, logistic-regression, metagenome, metagenomics, minhash, plasmids
- Language: Python
- Homepage:
- Size: 133 MB
- Stars: 6
- Watchers: 1
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
## Requirements
- numpy
- cython
- biopython
- click
- mmh3
- h5py
## Installation
```
git clone https://github.com/haradama/PlasmidPicker.git
cd PlasmidPicker
pip install -r requirements.txt
python setup.py install
```
## Usage
```
Usage: plasmidpicker pick [OPTIONS]
Detect plasmid sequence data in metagenome.
Options:
-i, --infile TEXT Specify FASTA input file
-t, --threshold INTEGER Threshold of probability (0 <= t <= 100) [70]
-l, --length INTEGER Threshold of contig's length [1000]
-d, --outdir TEXT Output directory [.]
--help Show this message and exit.
```
```
Usage: plasmidpicker classify [OPTIONS]
Perform similarity search of plasmids using MinHash.
Options:
-i, --infile TEXT Specify FASTA input file
-s, --sketch INTEGER Sketch size (1 <= s <=1000) [1000]
-l, --length INTEGER Threshold of contig's length [1000]
-hi, --hits INTEGER Number of hits to display [5]
-o, --outfile TEXT Output file [result.txt]
--help Show this message and exit.
```
## License