ALIGaToR - Annotator of Loci for IG and T-cell Receptors

A pipeline for annotating genomic contigs from the IG and TR loci. The pipeline includes:

• Extract: A parsing script that extracts gene, exon, and RSS name and corrdinates from reference annotations of choice of closely related species.

Important

Since publication of ALIGaToR, IMGT has chosen to block programmatic access to LIGM-DB in disregard of the pressing need for greater scientific exchange and in contravention of FAIR data principles. Annotations must therefore be retrieved through a browser (using a url of the form https://imgt.org/ligmdb/view.action?id=ACCESSION) and saved as local html file, which can then be passed to aligator extract using the new --local option.

• Predict: A prediction script calls submodule DnaGrep, that predicts RSS sequences based on genomic contigs.
• Annotate: Annotator script that uses the extracted reference genome and genomic information to generate a search databse for blast. Blast hits are matched with predicted RSSs. Other scripts are called to check for start and stop codons, and splice sites.

Dependencies/Prerequisites

• Python 3.6 or greater
• Muscle v3.8 (currently, muscle5 will cause an error)
• Blast+
• BedTools

Getting Started

After installing the above dependencies, clone the aligator repository:

	git clone https://github.com/scharch/aligator.git

Install required python packages:

	cd aligator
	pip install -r requirements.txt

Initialize the DnaGrep submodule:

	git submodule init
	git submodule update

Set enviromental variable:

	export ALIGATOR_PATH=$(pwd)

Quick help:

	aligator help

Alternatively, a Singularity container for ALIGaToR is available from Zenodo at https://doi.org/10.5281/zenodo.16004645

	singularity exec aligator.sif aligator <extract|predict|annotate> ...

Example commands and validation results:

Validate install (extract will fail due to IMGT blockade):

	bash validateInstall.sh

Re-run analysis from the paper (requires manual preparation and additional dependencies, see script header):

	bash sample_data/runPaperAnalysis.sh

Compare results to a reference (requires R with the packages bedtoolsr and ggalluvial):

	Rscript sample_data/gatorADE <reference annotations> <aligator output>

Citing:

If you use ALIGaToR, please cite: Schramm, Olubo, and Douek, "ALIGaToR: A tool for the automated annotation of immunoglobulin and T cell receptor genomic loci" Oxford Open Immunology, iqaf009