A Bioinformatics Pipeline for Analyses of Mycobacterium tuberculosis Whole Genome Sequencing Data
Aditi Gupta
Center for Emerging Pathogens, Rutgers University, Newark NJ 07103
Email: ag1349 [at] njms.rutgers.edu
October 18, 2017
Please see docs for tutorial on how to use SNPTB.
Citation information is in HOW_TO_CITE.
SNPTB is publicly available under the GNU GPL License.
SNPTB contains the following directories:
- code: contains all scripts
- software: contains Trimmomatic and FastQC software
- scheduler: contains script to run the SNPTB pipeline on SLURM job scheduler
- data: empty directory, option to save raw sequencing data here
- output: empty directory. When SNPTB is run, a new folder is created in "output" that contains a file with SNP annotation
- test: contains sample file that shows the format to specify pairs of samples for pairwise SNP identification
- H37Rv: all files of the reference Mycobacterium tuberculosis genome H37RV needed for running SNPTB