Comparative Genomics

This repository contains a set of comparative genomics scripts for Team II's comparative genomics group.

For general info, see the project's wiki page.

File Structure and Usage

The repository is organized as follows:

.
├── strain.sh               # Strain determination script
├── whole_genome            # Whole genome related scripts
│   ├── clustering          # Clustering based on whole genome similarity
│   ├── gwas                # Bacterial GWAS scripts and results
├── phylogeny               # Phylogeny related scripts
│   ├── ksnp                # kSNP scripts and results
│   ├── strain_detect       # Scripts and dependencies for strain detection
└

To determine strain of an assembled genome, run

./strain.sh -i assembly.fasta

Some of the scripts might only work on biogenome2018b.biology.gatech.edu server since they rely on specific files present on this server.

Dependencies

• All the necessary dependencies for strain.sh are present in the phylogeny/strain_detect directory.

• Database required for strain detection can be downloaded from:

  • pre-built Database (18GB)
  • pre-built Database (4GB)

  OR

  • A Klebsiella-specific (2.5GB) Database can be accessed on the biogenome2018b.biology.gatech.edu server at /projects/data/important_data/reference_DB/seeker_genomes/kleb_DB

• The database need to be put in the phylogeny/strain_detect/database directory