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README.md

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+<image src=https://github.com/scharch/aligator/assets/6708960/c6acd3d9-d082-4b0b-9f09-c99c7f8f651a>
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 # 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.
 
-## Getting Started
-Clone the aligator repository 
-git clone https://github.com/scharch/aligator.git
-
 ## Dependencies/Prerequisites 
-- Python
-- Beautifulsoup 4.12.3
+- Python 3.6 or greater
 - Muscle
 - Blast+
-- pyBedTools
-
-## Usage
-aligator --help
-### Example
-		 #Download BK063715 fasta file from IMGT.org
-		 #extract IGH annotations from IMGT's rheMac10 
-		 aligator extract https://imgt.org/ligmdb/view.action?id=BK063715 BK063715
+- 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`:
 
-		 #predict RSS for MF989451 and compare to sample data 
-		 aligator predict /sample_data /sample_data/MF989451.fa MF989451
+		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`:
 
-		 #annotate MF989451 and compare to sample data
-		 aligator annotate /sample_data/MF989451.fa /sample_data/MF989451.rss12_pred.bed MF989451.rss23_pred.bed IGH BK063715.fasta BK063715.bed --alleledb coding.fa --outgff annotations.gff --outfasta IgGenes.fa --blast blastn
+		aligator annotate $ALIGATOR_PATH/sample_data/MF989451.fa MF989451.RSS12.bed MF989451.RSS23.bed IGH BK063715.fasta BK063715.bed