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

Abstract Summary 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...

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Bibliographic Details
Published in:Bioinformatics 2020-08, Vol.36 (16), p.4510-4512
Main Authors: Isacchini, Giulio, Olivares, Carlos, Nourmohammad, Armita, Walczak, Aleksandra M, Mora, Thierry
Format: Article
Language:English
Subjects:
Family Characteristics
High-Throughput Nucleotide Sequencing
Humans
Life Sciences
Physics
Probability
Receptors, Antigen, B-Cell - genetics
Software
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Summary:Abstract Summary 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 post-selection probabilities of their sequences, as well as generate batches of synthetic sequences. The application also functions on mobile phones. Availability and implementation SOS is freely available to use at sites.google.com/view/statbiophysens/sos with source code at github.com/statbiophys/sos.
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btaa574