Metadata-Version: 2.1
Name: flight-genome
Version: 1.6.3
Summary: flight - metagenomic binner and variant clusterer.
Home-page: https://github.com/rhysnewell/flight
Author: Rhys Newell
Author-email: rhys.newell94@gmail.com
License: BSD-3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: umap-learn >=0.5.3
Requires-Dist: numpy <=1.24
Requires-Dist: scikit-learn <=1.1,>=1.0.2
Requires-Dist: scipy <=1.11
Requires-Dist: scikit-bio >=0.5.7
Requires-Dist: numba <=0.57,>=0.53
Requires-Dist: pandas >=1.3
Requires-Dist: pynndescent >=0.5.7
Requires-Dist: hdbscan >=0.8.28
Requires-Dist: joblib <=1.3.0
Requires-Dist: pebble
Requires-Dist: threadpoolctl
Requires-Dist: imageio
Requires-Dist: matplotlib
Requires-Dist: seaborn
Requires-Dist: tqdm
Requires-Dist: tbb
Requires-Dist: biopython

# Flight
The python component used by [Lorikeet](https://github.com/rhysnewell/Lorikeet) and [Rosella](https://github.com/rhysnewell/rosella)

# Installation
This module is only used in conjunction with other programs, but if you wish to install and play around with the code 
follow these instructions:

```
git clone https://github.com/rhysnewell/flight.git
cd flight
conda env create -n flight -f flight.yml
conda activate flight
pip install .
flight bin --help
```

# Requirements

Initial requirements for flight can be downloaded using the `flight.yml`:
```
conda env create -n flight -f flight.yml
```

# Usage

To perform mag recovery:
```
flight bin --assembly scaffolds.fasta --input coverm.cov --output output_dir/ --threads 24
```
