fiuzatayna / epitocore

EpitoCore

EpitoCore is a peptide-centric epitope prediction tool which takes into consideration pangenomic variation across strains of a given dataset, and reports conserved epitopes between homologues of those strains.

The EpitoCore program has been added to a Docker container in order to simplify installation.

This repository contains a Docker buildfile (Dockerfile) and folders with scripts and dependencies. To run this app the user must have admin rights.

To build the container

Clone this repository:

git clone https://github.com/fiuzatayna/epitocore
cd epitocore

Extract and enter docker folder:

tar -xf EpitoCore_docker.tar.xz
cd EpitoCore

Build docker container:

docker build -t epitocore .

Running an EpitoCore analysis

1. Enter the epitocore container:

docker run -v [local path or $PWD]/Output:/home/Output -it epitocore /bin/bash

You can open another terminal inside this same container using your running container id. Example: docker exec -it 109cff9ce41b bash

2. Open the command_sequence.sh script

nano command_sequence.sh

3. Insert species of interest name between the quotes in line

echo " " > species_file

4. Run command_sequence.sh script

./command_sequence.sh

The script will run each part of the code in sections until the IEDB immuno prediction is performed, then it will prompt:

• Number of strains
• Number of proteins
• Number of Alpha Transmembrane Domain Containing Proteins

Afterwards it will open a configuration_file file used by the R analysis and user must include

• IEDB consensus percentile rank thresholds
• Minimal number of strains in which a candidate peptide must be found
• Name of CMG Biotools clustering file

Additional

Inspect how many strains your species of interest has and other information with:

Count strains

ls get_proteome_output/ | wc -l

Count proteins

wc -l tmhmm_output/*

Count alpha transmembrane domain containing proteins

wc -l filtered_tmhmm_output/*

Open another terminal on the same container

docker exec -it [CONTAINERID] bash