nickp60 / gemini

:gem: Genome mining tool-- Identifies regions of atypicality

GEMINI

GEMINI is a genome mining tool, which detects regions of atypical nucleotide composition. It delineates compositional core (native) and accessory (alien) genome.

Usage

First set the permissions for the files

sudo chmod 775 gemini
sudo chmod 775 gemini.out

Program can now be run as

./gemini [options] genome.gbk output.txt

Add to Path

Add the following line to your $HOME/.bashrc file to make it available to all users:

export PATH=$PATH:'Path/to/GEMINI'

GEMINI can now be used from any folder as

gemini [options] genome.gbk output.txt

Input

Required input

GEMINI takes following two command-line arguments

1. Genome file in GenBank(full) format.
2. Name of Output file

Optional input

Following options can be used with the program

-h, --help shows help message and exit

-cite shows publication reference and exit

-info shows information about program and exit

-debug Keeps Temporary files

-verbose Prints on screen

-seg SEG Provide segmentation threshold in range 0-1

-clus1 CLUS1 Provide contiguous clustering threshold in range 0-1

-clus2 CLUS2 Provide non-contiguous clustering threshold in range 0-1

Output

GEMINI outputs a space separated file with six columns.

Column 1- GI-> Genomic island id

Column 2- Start-> Start co-ordinate of genomic island

Column 3- End-> End co-ordinate of genomic island

Column 4- Length-> Length of the genomic island

Column 5- Mosaic-> If a genomic island is mosaic (i.e. composed of more than one cluster) it is shown as 'M'.

Column 6- #genes-> Number of genes harbored on genomic island

Example

./gemini -debug -verbose -seg 0.999999999 -clus1 0.999999999999 -clus2 0.999999999999 example.gbk example_output.txt

Reference

GEMINI

Jani, Mehul, Kalai Mathee, and Rajeev K. Azad. "Identification of novel genomic islands in Liverpool epidemic strain of Pseudomonas aeruginosa using segmentation and clustering." Frontiers in microbiology 7 (2016).