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. 2022 Jul 14;94(29):10391–10399. doi: 10.1021/acs.analchem.2c01300

Figure 1.

Figure 1

Schematic overview of Stitch. (A) Input reads in PEAKS, Novor.Cloud or FASTA format are matched to user-defined templates for V/J/C segments of the heavy and light chains by local Smith–Waterman alignment. (B) For monoclonal antibodies, the top-scoring segments can be recombined for a second template-matching step on the full heavy and light chain sequences. (C) Procedure to reconstruct CDRH3 looks for an overlap between the overhanging reads extending the V- and J-segments. (D) Shared and unique reads are placed at the corresponding position in a cladogram of homologous template sequences to provide a quantitative overview of the template matching with explicit consideration of ambiguity in the read placement. This example is whole IgG from a COVID-19 hospitalized patient, as further described in Figure 4.