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. 2023 Mar 10;12:962945. doi: 10.3389/fcimb.2022.962945

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Copyright © 2023 Hurtado, Flynn, Lee, Salcedo, Cottrell, Skog, Burton, Nemazee, Schief, Landais, Sok and Briney

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Workflow of single cell multi-omics data processing using scab. Example commands are shown for several common data processing and analysis tasks. Briefly, starting with the unmodified output files from CellRanger, this sample workflow (1) reads CellRanger output data and annotates BCR sequences using abstar (Briney and Burton, 2018); (2) demultiplexes samples using cell hashes; (3) classifies BCR specificity using two AgBCs (“H1” and “H2”) and a single specificity group (“flu”), which includes both AgBCs; (4) assigns BCR sequences to clonal lineages using clonify (Briney et al., 2016); (5) writes the integrated AnnData object to file in h5ad format.