Phanatic v2.2.4

This python script (phanatic.py) will run a docker container to assemble genomes 'de novo' using SPAdes (version number below in third party software).

Associated publications:

1. Genome Sequences of Two Lytic Staphylococcus aureus Bacteriophages Isolated from Wastewater
2. Genome Sequence of a Lytic Staphylococcus aureus Bacteriophage Isolated from Breast Milk
3. Complete Genome Sequences of Four Pseudomonas aeruginosa Bacteriophages: Kara-mokiny 8, Kara-mokiny 13, Kara-mokiny 16, and Boorn-mokiny 1

FUNCTIONS

The main functions of phanatic are:

• De novo assembly for phages
• Reads quality checks run using fastqc
• Assembly quality and completeness check using CheckV
• Extraction of 'Complete' and 'High-quality' contigs (determined via assembly QC)
• OPTIONAL: Read mapping to host strains to check assembly contamination, generalised transduction
• Log file with each sample process detailed (phanatic_log.tsv)

Citation:

If you use this software please cite one of the papers below and look at the third party software to cite the correct versions of software utilised by this container.

https://journals.asm.org/doi/10.1128/mra.00954-22

https://journals.asm.org/doi/10.1128/mra.00953-22

Installation

To run this pipeline you first need a working docker installation.

Install using pip

pip install Phanatic==2.2.4

Run the help command to see options

phanatic.py -h

Run a basic assembly with default configuration

phanatic.py -i <PATH TO READS DIR> -o <PATH TO OUTPUT DIR>

Outputs

• Assembled genome
• CheckV analysis files
• SPAdes assembly files
• Reads QC files (fastqc)

Third-party software for base assembly

Software	Version	Description	Please cite
SPAdes	3.15.4	The St.Petersburg genome assembler containing various pipelines released under GPLv2	https://doi.org/10.1002/cpbi.102
bbmap	38.18	U.S Department of Energy (DOE) Joint Genome Institute (JGI) toolset containing a set of fast bioinformatic tools for DNA/RNA sequencing data	https://sourceforge.net/projects/bbmap/
biopython	1.78	A set of tools written in python for biological computation	https://biopython.org/
checkv	1.0.1	CheckV quality and completeness analysis for viral genomes	https://doi.org/10.1038/s41587-020-00774-7
checkv-db	1.5	Database version in this container	https://doi.org/10.1038/s41587-020-00774-7
fastqc	0.11.9	Quality control for reads	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Third-party software for read mapping (In addition to above assembly)

Software	Version	Description	Please cite
bwa	0.7.17	--------	--------
samtools	1.9	--------	--------

Docker tags

https://hub.docker.com/r/iszatt

License

GNU AGPLv3

Config file

This is the default config file, copy this and specify its location using '-c' to use your own with adjustments.

[phanatic]
image = iszatt/phanatic:2.2.4
author = 'Joshua J Iszatt'
citation = 'pending'

[pipeline]
normalise = True
filter = True
fastqc = True
barcode = False
mapping = True
re_assembly = True
identify_termini = False

[system]
RAM = 24000m

[input]
r1_ext = _R1.fastq.gz
r2_ext = _R2.fastq.gz

[trim]
read_length = 150
trim_length = 12
minimum_length = 100
read_quality = 15

[merge]
minimum_insert = 120
minimum_overlap = 20

[normalise]
target_coverage = 250

[SPAdes]
memory_gb = 24
threads = 24

[filter]
filter_length = 1000

[barcoding]
prefix = phage
barcode_length = 5

Host mapping file

An example csv formatted mapping file, notice that multiple sets of reads can be mapped to a single host genome. To use this: specify the path using the '--host_mapping' flag

host,read_1,read_2
hostA_genome.fasta,ReadsA1_R1.fastq.gz,ReadsA1_R2.fastq.gz
hostA_genome.fasta,ReadsA2_R1.fastq.gz,ReadsA2_R2.fastq.gz
hostB_genome.fasta,ReadsB1_R1.fastq.gz,ReadsB1_R2.fastq.gz