Biopolym. Cell. 2024; 40(3):218-218.
http://dx.doi.org/10.7124/bc.000AFC
Chronicle and Information
A comprehensive benchmarking study of adaptive immune receptor repertoire sequencing data aligners
1Iordachi F., 2Adamyan A., 3Bostan S., 4Krektun U., 5Calujac L., 5Dumitrescu C.
  1. Stanford University's OHS
    415, Broadway, Redwood City, CA 94063, USA
  2. Zaven and Sonia Akian College of Science and Engineering, American University of Armenia
    40, Marshal Baghramyan Ave., Yerevan, Armenia, 0019
  3. New School International School of Georgia
    35, Tskneti Hwy., Tbilisi, Georgia, 0162
  4. National Technical University of Ukraine "Igor Sikorsky Kyiv Polytechnic Institute"
    37, Beresteiskyi Ave, Kyiv, Ukraine, 03056
  5. Stefan cel Mare University of Suceava
    13, University Str., Suceava, Romania, 720229

Abstract

Aim. The reliability of Adaptive Immune Receptor Repertoire sequencing (AIRR–Seq) data analysis hinges on the performance of alignment tools, but due to frequent inconsistency in output formats and user experience, an objective comparison of AIRR data aligners is still missing. Thus, here we aimed to benchmark the most widely used AIRR–Seq data analysis tools – HighV–Quest, IgBlast, and MiXCR – and evaluate their alignment accuracy [1, 2]. Conclusions. Our study shows that based on the V–region overlap call, IgBlast achieves the best performance, with HighV–Quest and MiXCR following respectively. We also demonstrate that the distribution of V–region genes in reads has no statistically significant effect on the mapping outcome of each read.
Keywords: adaptive immune receptor repertoire, T cells, junctional diversity
Full text: (PDF, in English)

References

[1] Bolotin DA, Poslavsky S, Mitrophanov I, Shugay M, Mamedov IZ, Putintseva EV, Chudakov DM. MiXCR: software for comprehensive adaptive immunity profiling. Nat Methods. 2015; 12(5):380-1.
[2] Ye J, Ma N, Madden TL, Ostell JM. IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Res. 2013;41(Web Server issue):W34-40.