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arXiv · 2003.13149

SOS: Online probability estimation and generation of T and B cell receptors

Giulio Isacchini·Carlos Olivares·Armita Nourmohammad·Aleksandra M. Walczak·Thierry Mora
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Abstract

Recent advances in modelling VDJ recombination and subsequent selection of T and B cell receptors provide useful tools to analyze and compare immune repertoires across time, individuals, and tissues. A suite of tools--IGoR [1], OLGA [2] and SONIA [3]--have been publicly released to the community that allow for the inference of generative and selection models from high-throughput sequencing data. However using these tools requires some scripting or command-line skills and familiarity with complex datasets. As a result the application of the above models has not been available to a broad audience. In this application note we fill this gap by presenting Simple OLGA & SONIA (SOS), a web-based interface where users with no coding skills can compute the generation and post-selection probabilities of their sequences, as well as generate batches of synthetic sequences. The application also functions on mobile phones.

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Giulio Isacchini, Carlos Olivares, Armita Nourmohammad, Aleksandra M. Walczak, Thierry Mora. 2020-03-29. SOS: Online probability estimation and generation of T and B cell receptors. https://doi.org/10.1093/bioinformatics/btaa574

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