https://github.com/haradama/phash
Software to identify known plasmid sequence from metagenomic assembly using Minhash
https://github.com/haradama/phash
bioinformatics biology contigs fasta golang metagenome metagenomics minhash plasmid plasmids
Last synced: 3 months ago
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Software to identify known plasmid sequence from metagenomic assembly using Minhash
- Host: GitHub
- URL: https://github.com/haradama/phash
- Owner: haradama
- License: gpl-3.0
- Created: 2018-12-06T00:45:23.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2019-01-29T06:32:53.000Z (over 6 years ago)
- Last Synced: 2025-01-16T07:37:57.584Z (4 months ago)
- Topics: bioinformatics, biology, contigs, fasta, golang, metagenome, metagenomics, minhash, plasmid, plasmids
- Language: Go
- Homepage:
- Size: 15.9 MB
- Stars: 3
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
pHash is a software to identify known plasmid from metagenomic assembly with the very lightweight database.
## Installation
pHash is available in release page:(https://github.com/haradama/pHash/releases)
## Usage
Please download the plasmid database file on Zenodo: (http://doi.org/10.5281/zenodo.1991549)
```
Identifier of plasmid using database
Usage:
pHash identify [flags]
Flags:
-d, --db string Database
-h, --help help for identify
-i, --in string Input FASTA file
-k, --kmer int Length of k-mer (default 17)
-o, --out string Output FASTA file
-p, --paralell int Number of parallel processing (default 4)
-s, --sketch int Sketch size (default 1024)
-t, --threshold int Threshold of probability (default 10)
```
for example,
```
pHash identify -d PLASMID_DATABASE -i YOUR_METAGEMOMIC_DATA
```
If you want to build your own database, please execute the following command.
```
pHash makedb -i YOUR_PLASMID_DATA -o YOUR_DATABASE_NAME
```
## Test
```
sh ./tests/install_test_data.sh
pHash identify -d plasmidDB11062018.phash -i testData.fna
```
## License
[GNU General Public License v3.0](https://github.com/haradama/pHash/blob/master/LICENSE)