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SOS: online probability estimation and generation of T-and B-cell receptors

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Isacchini,  Giulio
Max Planck Research Group Statistical physics of evolving systems, Max Planck Institute for Dynamics and Self-Organization, Max Planck Society;

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Nourmohammad,  Armita
Max Planck Research Group Statistical physics of evolving systems, Max Planck Institute for Dynamics and Self-Organization, Max Planck Society;

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Citation

Isacchini, G., Olivares, C., Nourmohammad, A., Walczak, A. M., & Mora, T. (2020). SOS: online probability estimation and generation of T-and B-cell receptors. Bioinformatics, 36(16), 4510-4512. doi:10.1093/bioinformatics/btaa574.


Cite as: http://hdl.handle.net/21.11116/0000-0007-D836-9
Abstract
Recent advances in modelling VDJ recombination and subsequent selection of T- and B-cell receptors provide useful tools to analyse and compare immune repertoires across time, individuals and tissues. A suite of tools—IGoR, OLGA and SONIA—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 postselection probabilities of their sequences, as well as generate batches of synthetic sequences. The application also functions on mobile phones.