g2-compgenomics-team1

Add to your PATH: Roary Scoary Prokka SignalP Rnammer ...

filter_gwas.pl usage

This script is used to filter the Bacterialgwas with any P value and OR value that is disired.

perl filter_gwas.pl bacterialgawsoutput

run_prokka.sh usage

this script is to run prokka on multiple files automatically, an input of the list of the files you want to run is required.

bash run_prokka.sh filnamelist.txt

##wrapper script run_bacterialGWAS_pangenome.sh require bacterialGWAS: https://github.com/jessiewu/bacterialGWAS

##wrapper script run_kSNP.sh require kSNP3 installation with all dependencies: https://sourceforge.net/projects/ksnp/files/

plot_input.pl usage

this script is to help generate input file from Roary present_absent matrix to plot a Manhattan plot using R\

perl plot_input.pl roary_matrix

man_plot.R usage

generate Manhattan plot using the file generated by plot_input.pl

Rscript man_plot.R plot_input.txt

prepare_trait.sh usage

this file contains the command used in samtool SNP calling bash prepare_scoary_trait.sh phenotype.csv roary.output