ATTILA - AutomaTed Tool For Immunoglobulin Analysis

ATTILA searches for candidate immunoglobulin sequences in phage display libraries, generating as main output a list of sequences of heavy and light chain, which were selected by phage display experiment, and code for antibody fragments that can probably bind to the target molecule. ATTILA package has programs developed in C, Perl and Shell script to execute eight steps of a completely automated analysis.

ATTILA can analyse human sequences coding for variable domain of heavy (VH) and light chain (VL), produced by phage display technology. Therefore, the input for the method must be VH and VL libraries, from initial and final rounds. Considering that our approach uses distances between canonical aminoacid residues of variable domain based on human sequences, the analysis may also be performed on mouse sequences, since their distances are similar to those of human.

Requirements

In order to install and run ATTILA, you must have:

Linux system

Internet

FASTQC

Prinseq-lite

FastqJoin

Perl

IgBlast

R software

• R packages:
  • tidyverse: install.packages("tidyverse")
  • ggplot2: install.packages("ggplot2")
  • scales: install.packages("scales")

Installation

Docker install (recommended)

If you are using Docker, you just need to download the Dockerfile and type: docker build -t waldeyr/attila:v1.0 ..

Then, just run: docker run --memory="4096m" -ti waldeyr/attila:v1.0 bash

If you want to sharing a docker folder with your currently docker folder, run using: docker run -v $(pwd):/attila/shared --memory="2048m" -ti waldeyr/attila:v1.0 bash

Linux install

After installing all requirements, perform the following steps:

1. Download ATTILA package at https://github.com/waldeyr/attila/archive/master.zip

2. Uncompress the zip file using command line:

$ unzip attila-master.zip

3. Go to the directory where you want to install ATTILA, using cd command. Note that ATTILA and IgBlast packages must be subdirectories of the installation directory.

4. Type the following command line:

$ ln -s check_requirements.sh

Example: ln -s home/Attila/programs/check_requirements.sh check_requirements.sh

5. Run the following command line:

$ ./check_requirements.sh

If check requirements.sh prints "Type ./attilacli.sh to run ATTILA", then ATTILA is ready to run ! If not, check requirements.sh prints a list of requirements that still need to be installed.