(D) The fraction of the top 10 largest clones analyzed using SCIGA and Cell Ranger. 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. Keywords:software, single-cell, immunoglobulin repertoires, COVID-19, antibody == Background YKL-06-061 == The diversity of B-cell immunoglobulin is an important characteristic of the adaptive immune system. It is developed through the rearrangement of variable (V), diversity (D), and joining (J) gene segments, which is referred to as V(D)J; the pairing of heavy and light chains; and somatic hypermutation (SHM) [1]. Exposure to infections and environmental factors shapes the repertoire of B-cell immunoglobulins [24] and leads to clonal expansion of immune cells, allowing them to change into different types of cells to respond to a specific antigen. Understanding these immunoglobulin repertoires can help researchers to discover antibodies, monitor vaccination responses, and infer B-cell trafficking patterns [5,6]. 10X single-cell V(D)J sequencing is a powerful tool for investigating paired heavy and light chain repertoires of B-cell immunoglobulins [7]. It has been used in the identification of neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 YKL-06-061 (SARS-CoV-2) [8], the virus that causes coronavirus disease 2019 (COVID-19) [9]. However, accurately analyzing 10X single-cell immunoglobulin repertoires remains a challenge owing to the high diversity of immunoglobulin repertoires and the lack of CD14 specialized software that YKL-06-061 can analyze such diverse data. Here, we developed SCIGA (Single-Cell Immunoglobulin Repertoire Analysis), a software package for quickly analyzing the data of 10X single-cell immunoglobulin repertoires. SCIGA performs read trimming, immunoglobulin sequence assembly and annotation, and heavy and light chain pairing by means of a 1-line command. It also computes the statistics of repertoires, including gene usage frequency, SHM rate, length of complementarity-determining region 3 (CDR3), and clonality, and further implements visualization. We profiled the immunoglobulin repertoires of peripheral blood mononuclear cells (PBMCs) from 9 patients with COVID-19 using SCIGA. Finally, we identified 4 neutralizing antibodies against SARS-CoV-2 from these repertoires. == Methods == SCIGA is a software package for the analysis of 10X single-cell immunoglobulin repertoires. It integrates several tools and algorithms into a single workflow. The input data can be raw reads or the output of Cell Ranger (RRID:SCR_017344) [10]. The details of the SCIGA algorithm can be found in theSupplementary Methods and Materials. Briefly, the workflow, which is summarized in Fig.1, is as follows. (i) Quality control of reads: trim the reads of low quality using Trimmomatic (RRID:SCR_011848) [11]. (ii) Call cell: the 10X system generates a large amount of Gel Beads-in-Emulsion (GEMs) that contain no cell. We need to identify the cell-containing GEMs before further analysis. SCIGA considers the GEMs containing cell(s) when the YKL-06-061 read number of the GEMs exceeds a threshold (seeSupplementary Methods and Materials). (iii) Immunoglobulin sequence assembly: the immunoglobulin sequences for each cell were assembled using SSAKE (RRID:SCR_010753) [12], which is a reliablede novoassembler for short reads. (iv) Gene call: to detect the usage of the V(D)J gene and C gene (isotype), SCIGA aligns the assembled immunoglobulin sequences against the V-, YKL-06-061 D-, and J- gene reference database using IgBLAST (RRID:SCR_002873) [13] and against C-gene reference database using BLAST (RRID:SCR_004870) [14]. The V(D)JC reference databases for humans, mice, and rats were downloaded from the international ImMunoGeneTics information system (IMGT) [15] and embedded in the SCIGA software. (v) Quality control of the immunoglobulin sequence: only the immunoglobulins that are complete, in the correct reading frame, and have no stop codon are retained. (vi) Quality control of the cells: after immunoglobulin sequence assembly and filtering, some cells have multiple heavy or light chains, whereas some cells have only 1 1 chain. SCIGA reports the heavy and light.