Skip to content

Software to identify plasmid sequence data from metagenome using logistic regression and Minhash

License

Notifications You must be signed in to change notification settings

haradama/PlasmidPicker

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

32 Commits
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

PlasmidPicker

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

About

Software to identify plasmid sequence data from metagenome using logistic regression and Minhash

Topics

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published