ALIGaToR: A tool for the automated annotation of immunoglobulin and T cell receptor genomic loci

Abstract Advances in sequencing technology have made it possible to capture complex immunogenetic loci at a scale that exceeds the capacity for manual annotation. Here we present the Annotator of Loci for ImmunoGlobulins and T cell Receptors (ALIGaToR), an automated pipeline to transfer genetic annotations from a known reference to a novel genomic assembly. We show that ALIGaToR accurately reproduces manually curated annotations and is capable of transferring labels even between distantly related species. Code and documentation for ALIGaToR, including a script reproducing all analyses in this paper, are available at https://github.com/scharch/aligator. Competing Interest Statement The authors have declared no competing interest. Footnotes Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license.