Long read assembly for phages:
Figure 1: Rough phage assembly pipeline, dotted line indicates where processing begins.
- Download the yml environment file:
wget https://anaconda.org/JoshIszatt/phunky/2024.05.24.145220/download/phunky.yml
- Create the environment
conda env create --file phunky.yml
- Activate the environment:
conda activate phunky
- Install phunky pipeline:
pip install phunky
- Optional: Setup the checkv database
checkv download_database /path/to/checkv-db
export CHECKVDB=/path/to/checkv-db
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/')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
- 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
- Create conda distribution
- Add hash key function