SCIGA: Software for large-scale, single-cell immunoglobulin repertoire analysis. Issue 9 (28th September 2021)

• Record Type: Journal Article
• Authors: Ye, Haocheng; Cheng, Lin; Ju, Bin; Xu, Gang; Liu, Yang; Zhang, Shuye; Wang, Lifei; Zhang, Zheng
• Is Part Of: GigaScience. Volume 10:Issue 9(2021)
• Publication Date: 2021-09-28
• Subjects: software -- single-cell -- immunoglobulin repertoires -- COVID-19 -- antibody; Information storage and retrieval systems -- Research -- Periodicals; Biology -- Research -- Periodicals; Medical sciences -- Research -- Periodicals; Database management -- Periodicals; 570.285
• DOI: 10.1093/gigascience/giab050
• Languages: English
• ISSNs: 2047-217X

Abstract

Abstract: Background: B-cell immunoglobulin repertoires with paired heavy and light chain can be determined by means of 10X single-cell V(D)J sequencing. Precise and quick analysis of 10X single-cell immunoglobulin repertoires remains a challenge owing to the high diversity of immunoglobulin repertoires and a lack of specialized software that can analyze such diverse data. Findings: In this study, specialized software for 10X single-cell immunoglobulin repertoire analysis was developed. SCIGA (Single-Cell Immunoglobulin Repertoire Analysis) is an easy-to-use pipeline that performs read trimming, immunoglobulin sequence assembly and annotation, heavy and light chain pairing, statistical analysis, visualization, and multiple sample integration analysis, which is all achieved by using a 1-line command. Then SCIGA was used to profile the single-cell immunoglobulin repertoires of 9 patients with coronavirus disease 2019 (COVID-19). Four neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were identified from these repertoires. Conclusions: SCIGA provides a complete and quick analysis for 10X single-cell V(D)J sequencing datasets. It can help researchers to interpret B-cell immunoglobulin repertoires with paired heavy and light chain.