{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T20:54:15Z","timestamp":1781211255981,"version":"3.54.1"},"reference-count":59,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2024,11,4]],"date-time":"2024-11-04T00:00:00Z","timestamp":1730678400000},"content-version":"vor","delay-in-days":42,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100012579","name":"ISF","doi-asserted-by":"publisher","award":["2940\/21"],"award-info":[{"award-number":["2940\/21"]}],"id":[{"id":"10.13039\/100012579","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Ministry of Innovation, Science & Tecnology","award":["1001576181\/0004941"],"award-info":[{"award-number":["1001576181\/0004941"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,9,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) is critical for our understanding of the adaptive immune system\u2019s dynamics in health and disease. Reliable analysis of AIRR-seq data depends on accurate rearranged immunoglobulin (Ig) sequence alignment. Various Ig sequence aligners exist, but there is no unified benchmarking standard representing the complexities of AIRR-seq data, obscuring objective comparisons of aligners across tasks. Here, we introduce GenAIRR, a modular simulation framework for generating Ig sequences alongside their ground truths. GenAIRR realistically simulates the intricacies of V(D)J recombination, somatic hypermutation, and an array of sequence corruptions. We comprehensively assessed prominent Ig sequence aligners across various metrics, unveiling unique performance characteristics for each aligner. The GenAIRR-produced datasets, combined with the proposed rigorous evaluation criteria, establish a solid basis for unbiased benchmarking of immunogenetics computational tools. It sets up the ground for further improving the crucial task of Ig sequence alignment, ultimately enhancing our understanding of adaptive immunity.<\/jats:p>","DOI":"10.1093\/bib\/bbae556","type":"journal-article","created":{"date-parts":[[2024,10,19]],"date-time":"2024-10-19T15:16:50Z","timestamp":1729351010000},"source":"Crossref","is-referenced-by-count":5,"title":["An unbiased comparison of immunoglobulin sequence aligners"],"prefix":"10.1093","volume":"25","author":[{"given":"Thomas","family":"Konstantinovsky","sequence":"first","affiliation":[{"name":"Faculty of Engineering, Bar Ilan University , 5290002 Ramat Gan,","place":["Israel"]},{"name":"Bar Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University , 5290002 Ramat Gan,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ayelet","family":"Peres","sequence":"additional","affiliation":[{"name":"Faculty of Engineering, Bar Ilan University , 5290002 Ramat Gan,","place":["Israel"]},{"name":"Bar Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University , 5290002 Ramat Gan,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pazit","family":"Polak","sequence":"additional","affiliation":[{"name":"Faculty of Engineering, Bar Ilan University , 5290002 Ramat Gan,","place":["Israel"]},{"name":"Bar Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University , 5290002 Ramat Gan,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gur","family":"Yaari","sequence":"additional","affiliation":[{"name":"Faculty of Engineering, Bar Ilan University , 5290002 Ramat Gan,","place":["Israel"]},{"name":"Bar Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University , 5290002 Ramat Gan,","place":["Israel"]},{"name":"Department of Pathology, Yale School of Medicine , New Haven, CT,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,11,2]]},"reference":[{"key":"2024112010175253200_ref1","doi-asserted-by":"crossref","DOI":"10.1201\/9781315533247","volume-title":"Janeway\u2019s Immunobiology","author":"Murphy","year":"2016"},{"key":"2024112010175253200_ref2","doi-asserted-by":"publisher","first-page":"1019","DOI":"10.1038\/ni1007-1019","article-title":"The clonal selection theory: 50 years since the revolution","volume":"8","author":"Hodgkin","year":"2007","journal-title":"Nat Immunol"},{"key":"2024112010175253200_ref3","doi-asserted-by":"publisher","first-page":"573","DOI":"10.1038\/nri1896","article-title":"Targeting of somatic hypermutation","volume":"6","author":"Odegard","year":"2006","journal-title":"Nat Rev Immunol"},{"key":"2024112010175253200_ref4","doi-asserted-by":"publisher","first-page":"e134","DOI":"10.1093\/nar\/gks457","article-title":"Quantifying selection in 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