UNIQmin: An alignment-independent tool for the study of viral sequence diversity at any given rank of taxonomy lineage

Brief Description

Sequence variation among viruses, even of a single amino acid, can expand their host repertoire or enhance the infection ability. Alignment-independent or -free approach represents an alternative to the study of viral diversity, which is devoid of the need for sequence conservation to perform comparative analyses. Herein, we present UNIQmin, a tool that utilises an alignment independent method to generate the minimal set of viral sequences, as a way to study their diversity, across any rank of taxonomic lineage. The minimal set refers to the smallest possible number of sequences required to capture the entire repertoire of viral peptidome diversity present in the given sequence dataset.

Step-by-step of UNIQmin
Figure Scheme
UNIQmin as a Package
Citing Resources
Found a Bug

Step-by-step of UNIQmin

UNIQmin comprises of five execution steps, with a Python script for each step. These scripts are provided in the PythonScript folder, accompanied with detailed explanations for the algorithm and execution of each step. The sample input file (exampleinput.fas) and example output file (exampleoutput.fasta) are also provided.

Figure Scheme

UNIQmin as a Package

Installation

via pip
```
pip install uniqmin
```
via package clone from GitHub repository
```
git clone https://github.com/ChongLC/MinimalSetofViralPeptidome-UNIQmin.git
```
Note for users who use Conda environment (e.g.: via Jupyter Notebook):
Before pip install of the package, run
```
conda config --add channels conda-forge
conda install pyahocorasick
```
... and restart the kernel to use the updated package. Then, run
```
pip install uniqmin
```

Upgrade installed version

pip install uniqmin --upgrade

Usage

uniqmin [-h] [-i INPUT] [-o OUTPUT] [-k KMERLENGTH] [-t THREADS]

A sample usage:
The UNIQmin tool is applied to generate a minimal set (to be saved in an output folder, named "result") for a sample input file (named "exampleinput.fas") with a k-mer window size parameter of nine (9; nonamer) and utilising 4-threads of a CPU (subject to limitations of the resource used):

uniqmin -i exampleinput.fas -o result -k 9 -t 4

Command-line Arguments

Argument	Parameter	Type	Required	Default	Description
-h	help	N/A	FALSE	N/A	Show this help message and exit
-i	sequence input file	String	TRUE	N/A	Path of the input file (in FASTA format)
-o	output directory name	String	TRUE	N/A	Directory to store the output file to be created
-k	k-mer window size	Integer	FALSE	9	The length of the constituent k-mer to be used
-t	number of threads	Integer	FALSE	4	The number of CPU threads to be used

Citing Resources

For original reference, please refer to our paper:
Chong, L.C.; Lim, W.L.; Ban, K.H.K.; Khan, A.M. An Alignment-independent Approach for the Study of Viral Sequence Diversity at Any Given Rank of Taxonomy Lineage. Biology 2021, 10, 853. doi: 10.3390/biology10090853
For a protocol describing the step-by-step utility of UNIQmin, please refer to our preprint:
Chong, L.C.; Khan, A.M. UNIQmin, An Alignment-free Tool to Study Viral Sequence Diversity across Taxonomic Lineages: A Case Study of Monkeypox Virus. bioRxiv 2022.08.09.503271. doi: 10.1101/2022.08.09.503271
For application of UNIQmin to study SARS-CoV-2 lineage diversity, please refer to our preprint:
Chong, L.C.; Khan, A.M. Negligible Peptidome Diversity of SARS-CoV-2 and its Higher Taxonomic Ranks. bioRxiv 2022.10.31.513750. doi: 10.1101/2022.10.31.513750

Found a bug?

Or would you like a feature to be added? Or maybe drop some feedback? Just open a new issue or send an email to us (lichuinchong@gmail.com).

ChongLC/MinimalSetofViralPeptidome-UNIQmin