Phunky

Long read assembly for phages: Figure 1: Rough phage assembly pipeline, dotted line indicates where processing begins.

Install dependencies

1. Download the yml environment file:

wget https://anaconda.org/JoshIszatt/phunky/2024.05.24.145220/download/phunky.yml

2. Create the environment

conda env create --file phunky.yml

3. Activate the environment:

conda activate phunky

4. Install phunky pipeline:

pip install phunky

5. Optional: Setup the checkv database

checkv download_database /path/to/checkv-db

export CHECKVDB=/path/to/checkv-db

Usage

Open a python terminal and enter:

import phunky
dir(phunky)

Quick phage assembly:

import phunky

phunky.assembly_pipeline('example_reads.bam', 'output_directory/')

Batch phage assembly:

import phunky
phunky.batch_assembly_pipeline('reads_directory/', 'output_directory/')

Citation:

There is a CITATION file in this repository (.CFF), however Phunky may also be cited like so:

Iszatt, Joshua James. (2024). PHUNKY long read assembly pipeline (Version v0.3) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.13981020

Dependencies:

• python>=3
• checkv==1.0.3
• biopython==1.83
• bbmap==39.06
• pandas==2.2.1
• matplotlib==3.8.4
• flye==2.9.3
• porechop_abi==0.5.0
• nanoplot==1.42.0
• filtlong==0.2.1

General todo

• Create conda distribution
• Add hash key function