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bioRxiv · 10.1101/2025.05.02.651960

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

Schramm, C. A.·Olubo, S.·Douek, D. C.
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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.

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Schramm, C. A., Olubo, S., Douek, D. C.. 2025-05-08. ALIGaToR: A tool for the automated annotation of immunoglobulin and T cell receptor genomic loci. https://doi.org/10.1101/2025.05.02.651960

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