flight-genome 1.0.0

flight - metagenomic binner and variant clusterer.

Flight

The python component used by Lorikeet and 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