The ab[x] toolkit is a comprehensive suite of software tools for processing, annotating and analyzing antibody repertoire data. At the core of the ab[x] toolkit is abstar, a robust tool for performing large-scale sequence pre-processing, germline gene assignment and primary annotation. Similar in function to IMGT’s High/V-QUEST, abstar is not throughput limited, capable of readily processing billions of antibody sequences. If you’d like to cite the ab[x] tookit, please reference the following manuscript:
Massively scalable genetic analysis of antibody repertoires
Briney B, Burton DR
bioRxiv 2018 Oct 19. doi: 10.1101/447813
Unseeded clonal lineage assignment, the process of assigning all antibody sequences in a dataset to the appropriate clonal lineage, is a complex task. Accurate lineage assignment on highly mutated lineages, in which clonal siblings may differ by as much as 20% as is the case in chronic HIV infection, is substantially more difficult. We have developed clonify, which is able to perform unseeded clonal lineage assignment on large-scale antibody heavy chain datasets. If you’d like to cite clonify, please reference the following manuscript:
Clonify: unseeded antibody lineage assignment from next-generation sequencing data
Briney B, Le K, Zhu J, Burton DR
Sci Rep. 2016 Apr 22;6:23901. doi: 10.1038/srep23901
Unseeded antibody clonal lineage assignment on large-scale antibody heavy chain sequence datasets.