Phanta

Configurable short read assembly pipeline 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/phanta/2024.05.31.130738/download/phanta.yml

2. Create the environment

conda env create --file phanta.yml

3. Activate the environment:

conda activate phanta

4. Install phanta pipeline:

pip install phanta

5. Optional: Set up the checkv database

checkv download_database /path/to/checkv-db

export CHECKVDB=/path/to/checkv-db

Usage

Open a python terminal and enter:

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

import phanta
reads = phanta.detect_reads('path_to_input_directory/')

Single phage assembly (Uses the default configurations below if no config parameter is specified):

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):

import phanta
phanta.batch_assembly_pipeline('path_to_input_directory/', 'output_directory/', config_file='/path_to_config.json')

Reads QC only:

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 JJ. PHANTA short read assembly pipeline. Published online June 2024. Version <VERSION>. Accessed <ACCESS DATE>. https://github.com/JoshuaIszatt/phanta

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

{
 "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"
 }
}