IgMAT: immunoglobulin sequence multi-species annotation tool for any species including those with incomplete antibody annotation or unusual characteristics.

Abstract

The advent and continual improvement of high-throughput sequencing technologies has made immunoglobulin repertoire sequencing accessible and informative regardless of study species. However, to fully map changes in polyclonal dynamics, precise annotation of these constantly rearranging genes is pivotal. For this reason, data agnostic tools able to learn from presented data are required. Most sequence annotation tools are designed primarily for use with human and mouse antibody sequences which use databases with fixed species lists, applying very specific assumptions which select against unique structural characteristics. We present IgMAT, which utilises a reduced amino acid alphabet, incorporates multiple HMM alignments into a single consensus and enables the incorporation of user defined databases to better represent their species of interest. Availability and implementationIgMAT has been developed as a python module, and is available on GitHub (https://github.com/TPI-Immunogenetics/igmat) for download under GPLv3 license. Supplementary informationModel Breakdowns