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.
• 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
• Blast+
• BedTools

Getting Started

Clone the aligator repository:

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

Install required python packages:

	pip install -r aligator/requirements.txt

Set enviromental variable:

	export ALIGATOR_PATH=$(pwd)/aligator

Quick help:

	`aligator help`

Vignette annotating MF989451 from Ramesh et al Frontiers Immunology 2017:

Data is in aligator/sample_data.

First, get reference genome from IMGT:

	#Download BK063715 fasta file from https://imgt.org/ligmdb/view.action?format=FASTA&id=BK063715
	#Then create bedfile with reference annotations
	aligator extract https://imgt.org/ligmdb/view.action?id=BK063715 BK063715

Find possible RSS motifs in the target contig. For MF989451, the output should look the same as sample_data/MF989451.rss12_pred.bed and sample_data/MF989451.rss23_pred.bed:

	aligator predict $ALIGATOR_PATH/sample_data/MF989451.fa MF989451

Finally, annotate the target contig. For MF989451, the actual annotations provided by Ramesh et al are included as sample_data/MF989451.ground_truth.bed:

	aligator annotate $ALIGATOR_PATH/sample_data/MF989451.fa MF989451.RSS12.bed MF989451.RSS23.bed IGH BK063715.fasta BK063715.bed