flight-genome


Nameflight-genome JSON
Version 1.0.1 PyPI version JSON
download
home_pagehttps://github.com/rhysnewell/rosella
Summaryflight - metagenomic binner and variant clusterer.
upload_time2021-01-17 12:01:57
maintainer
docs_urlNone
authorRhys Newell
requires_python
licenseBSD-3
keywords
VCS
bugtrack_url
requirements No requirements were recorded.
Travis-CI No Travis.
coveralls test coverage No coveralls.
            # Flight
The python component used by [Lorikeet](https:/github.com/rhysnewell/Lorikeet) and [Rosella](https:/github.com/rhysnewell/rosella)
It can be used as a standalone binning algorithm for MAGs, but will not include contig SNP information
which is collected by 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
```



            

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    "description": "# Flight\nThe python component used by [Lorikeet](https:/github.com/rhysnewell/Lorikeet) and [Rosella](https:/github.com/rhysnewell/rosella)\nIt can be used as a standalone binning algorithm for MAGs, but will not include contig SNP information\nwhich is collected by Rosella.\n# Installation\nThis module is only used in conjunction with other programs, but if you wish to install and play around with the code \nfollow these instructions:\n\n```\ngit clone https://github.com/rhysnewell/flight.git\ncd flight\nconda env create -n flight -f flight.yml\nconda activate flight\npip install .\nflight bin --help\n```\n\n# Requirements\n\nInitial requirements for flight can be downloaded using the `flight.yml`:\n```\nconda env create -n flight -f flight.yml\n```\n\n# Usage\n\nTo perform mag recovery:\n```\nflight bin --assembly scaffolds.fasta --input coverm.cov --output output_dir/ --threads 24\n```\n\n\n",
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