*figure adapted from LANL's HIV-1 Gene Map
A tool to help visualize the variability of a nucleic acid sequence (genome, gene, etc).
The variability of a region is assessed by calculating the Shannon entropy of each position in the region. Usually, insertions and deletions are ignored and only non-ambiguous nucleotides are considered. However, this tool can include both insertions and deletions in the entropy calculation. This is simply done by determining the "object" at each position (insertion, deletion, or single nucleotide), calculating the frequency of each object (f), and running the frequencies through the Shannon entropy formula: -sum(f*log(f)).
Ambiguous nucleotides are proportionally converted to all their non-ambiguous nucleotides. For example, if at a position, there is a N nucleotide observation, then 1 N is counted as 0.25 A, 0.25 C, 0.25 G, and 0.25 T. For insertions with ambiguous nucleotides, all non-ambiguous permutations are proportionally considered. (If the number of permutations grow beyond 10000, then the entropy calculation will simply use the ambiguous insertion).
Simply download this repository!
git clone https://github.com/ArmaanAhmed22/VariabilityAnalyzer.git
An input, aligned reference sequence and quasispecies files should be placed within Input/{file}, where {file} is the name of the region-to-be-analyzed (protease, SARS-CoV-2, HIV-1, etc, etc).
Next, run snakemake Output/{file}/variability_map.png -c1 to generate the output files.
In the Pipeline/SETTINGS.json file, the following can be toggled:
-
INCLUDE_AMGIGUOUS_NUCLEOTIDES (true/false): Whether or not to include ambiguous nucleotides in the entropy calculation. -
ROLLING_AVERAGE_WINDOW (int): The length of the window included in the rolling average. Numbers<=0will remove the rolling average.
Directory:
Input/
Example/
reference.fasta
quasispecies.fasta
Pipeline/**
Snakefile
Run snakemake Output/Example/variability_map.png -c1 to generate variability_map.png and variability_map.csv
