Using the base-percentage space spectrum of the 10-mer decomposition of genomic and plasmid DNA to classify bacteria strains
Our analysis requires the use of jellyfish to count the number of unique k-mers in a genome sequence. Get the source code directly by by preforming a wget on the source code link which can be found on their git repo here.
User guide for the jellyfish software can be found here. Jelly fish software is developed by Guillaume Marçais or Carl Kingsfor.
In order to run our analysis, the following R libraries need to be installed:
- tidyr
- readr
- dplyr
- mlr
- ggplot2
Download these packages using the R packages.install() command before running the analysis script
Code for analysis is all automated and contained in the runModel shell script of the home directory of the repository.