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. Author manuscript; available in PMC: 2023 Jul 13.
Published in final edited form as: Nat Protoc. 2022 Nov 16;18(2):396–423. doi: 10.1038/s41596-022-00766-8

Extended Data Fig. 2. Bioinformatic pipeline for design of the PepSeq library and analysis of sequencing results.

Extended Data Fig. 2

Graphical depiction of a typical analysis workflow through peptide design and encoding (left) and bioinformatic analysis (right). Each box represents a step in the bioinformatic pipeline and includes a basic description of the step, along with a recommended piece of software (left) or PepSIRF module (right) for accomplishing the described step (contained in square brackets). Arrows indicate a direct connection, with the output file from the upstream box being used as an input file for the downstream box. The dashed box indicates a step that needs to be performed the first time running the analysis but is not required to be run for every analysis.