Data

Tools

Indexes

Applications

Experiments

Open Source Science

phunky

Nanopore long read assembly data pipeline for phage genomes

https://github.com/joshuaiszatt/phunky

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.7%) to scientific vocabulary

Keywords

bioinformatics bioinformatics-pipeline bioinformatics-tool genome-assembly genomics nanopore oxford-nanopore phage phage-genomes
Last synced: 4 months ago · JSON representation ·

Repository

Nanopore long read assembly data pipeline for phage genomes

Basic Info
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 2
Topics
bioinformatics bioinformatics-pipeline bioinformatics-tool genome-assembly genomics nanopore oxford-nanopore phage phage-genomes
Created over 1 year ago · Last pushed 7 months ago
Metadata Files
Readme Changelog Contributing Citation

README.md

Phunky

DOI

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

Python

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: py import phunky dir(phunky)

Quick phage assembly:

```py import phunky

phunky.assemblypipeline('examplereads.bam', 'output_directory/') ```

Batch phage assembly: py 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

Owner

  • Name: Joshua Iszatt
  • Login: JoshuaIszatt
  • Kind: user
  • Location: Perth

PhD candidate. Interested in microbial genomics and protein structures. https://www.researchgate.net/profile/Joshua-Iszatt

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: "Iszatt"
    given-names: "Joshua James"
    orcid: "https://orcid.org/0000-0002-6394-5058"
title: "PHUNKY long read assembly pipeline"
version: "v0.3"
identifiers:
  - type: doi
    value: 10.5281/zenodo.13981020
url: "https://github.com/JoshuaIszatt/phunky"
date-released: 2024-06-20

GitHub Events

Total
  • Release event: 1
  • Push event: 2
  • Create event: 2
Last Year
  • Release event: 1
  • Push event: 2
  • Create event: 2

Dependencies

setup.py pypi
conda_recipe/meta.yml cpan