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phanta

Illumina short read assembly data pipeline for phage

https://github.com/joshuaiszatt/phanta

Science Score: 67.0%

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    Found 4 DOI reference(s) in README
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    Links to: zenodo.org
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    Low similarity (10.4%) to scientific vocabulary

Keywords

bioinformatics bioinformatics-pipeline bioinformatics-tool genome-analysis genome-assembly genomics illumina illumina-sequencing phage phage-genomes
Last synced: 4 months ago · JSON representation ·

Repository

Illumina short read assembly data pipeline for phage

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Topics
bioinformatics bioinformatics-pipeline bioinformatics-tool genome-analysis genome-assembly genomics illumina illumina-sequencing phage phage-genomes
Created over 1 year ago · Last pushed 5 months ago
Metadata Files
Readme Changelog Contributing Citation

README.md

Phanta

DOI

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

Install dependencies

  1. Create the environment sh conda env create --file phanta.yml

  2. Activate the environment: sh conda activate phanta

  3. Install phanta pipeline: sh pip install phanta

  4. Optional: Set up the checkv database sh checkv download_database /path/to/checkv-db

sh export CHECKVDB=/path/to/checkv-db

Usage

Open a python terminal and enter: py import phanta dir(phanta)

Detect reads: This will return a list of Reads class objects that can be passed individually or as a batch to assembly pipelines py import phanta reads = phanta.detect_reads('path_to_input_directory/')

Single phage assembly (Uses the default configurations below if no config parameter is specified): py import phanta reads = phanta.detect_reads('path_to_input_directory/') phanta.assembly_pipeline(reads[0], 'output_directory/')

Batch phage assembly (Using your own edited config file): py import phanta phanta.batch_assembly_pipeline('path_to_input_directory/', 'output_directory/', config_file='/path_to_config.json')

Reads QC only: py import phanta phanta.batch_assembly_pipeline('path_to_input_directory/', 'output_directory/', qc_only=True)

Citation:

There is a CITATION file in this repository (.CFF), however Phanta may also be cited like so: Iszatt, Joshua James. (2024). PHANTA short read assembly pipeline (Version v0.3) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.13981011

Dependencies:

  • python>=3
  • checkv==1.0.3
  • biopython==1.83
  • bbmap==39.06
  • pandas==2.2.1
  • matplotlib==3.8.4
  • spades==3.15.5
  • fastqc==0.12.1
  • multiqc==1.22.1
  • pilon==1.24
  • packaging
  • deprecated

Configuration

These are the defaults, amend as required and pass to the pipeline functions json { "system": { "RAM": 24000, "threads": 8 }, "input": { "interleaved_ext": "_interleaved.fastq", "r1_ext": "_R1.fastq.gz", "r2_ext": "_R2.fastq.gz" }, "reads": { "read_length": 150, "trim_length": 10, "minimum_length": 100, "read_quality": 30, "error_correction": true, "target_coverage": 200 }, "assembly": { "kmers": "55,77,99,127" }, "extraction": { "mincov": 60, "minlen": 4000, "mincomplete":90 } }

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: "PHANTA short read assembly pipeline"
version: "v0.3"
identifiers:
  - type: doi
    value: 10.5281/zenodo.13981011
url: "https://github.com/JoshuaIszatt/phanta"
date-released: 2024-06-25

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Dependencies

setup.py pypi