This pipeline is designed by comparative genomic team of group 1, to analyse genomic features of different organisms
1. python3
2. mentalist needs to be on your path
3. pandas install
4. tcsh
5. kSNP3 appended to path
6. MASH appended to path
Mentalist installation:
The instruction of installing Mentalist is described from the website https://github.com/WGS-TB/MentaLiST
kSNP3 installation:
Please follow the installation guide: http://gensoft.pasteur.fr/docs/kSNP3/01/kSNP3.01%20User%20Guide%20.pdf
MASH installation:
Please follow the installation guide: https://github.com/marbl/Mash/blob/master/INSTALL.txt
git clone https://github.gatech.edu/compgenomics2019/Team1-ComparativeGenomics.git
cd Team1-ComparativeGenomics
To run cgMLST: ./comparativePipeline.py (or python comparativePipeline.py ) -m - i<name of input> -o <name of output> -db <name of database>
To calculate difference for cgMLST: ./comparativePipeline.py (or python comparativePipeline.py) -diff -i <name of cgMLST output>
-i : name of input file
-o : name of output file
-m : to run cgMLST
-diff: to calculate differences for cgMLST result
-k : to run kSNP3
-mash : to run MASH