the ab[x] toolkit

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

abstar

VDJ assignment and antibody sequence annotation. Scalable to billions of sequences.

abutils

Primitives and utilities for interactive antibody repertoire analysis

abcloud

Launch, configure and manage cloud computing resources using Amazon's EC2.

abtools

Secondary analysis of antibody repertoire sequencing data

clonify

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

clonify

Unseeded antibody clonal lineage assignment on large-scale antibody heavy chain sequence datasets.