phippery: a software suite for PhIP-Seq data analysis

Abstract

Summary: We present the phippery software suite for analyzing data from phage display methods that use immunoprecipitation and deep sequencing to capture antibody binding to peptides, often referred to as PhIP-Seq. It has three main components that can be used separately or in conjunction: (i) a Nextflow pipeline, phip-flow, to process raw sequencing data into a compact, multidimensional dataset format and allows for end-to-end automation of reproducible workflows. (ii) a Python API, phippery, which provides interfaces for tasks such as count normalization, enrichment calculation, multidimensional scaling, and more, and (iii) a Streamlit application, phip-viz, as an interactive interface for visualizing the data as a heatmap in a flexible manner.

Availability and implementation: All software packages are publicly available under the MIT License. The phip-flow pipeline: https://github.com/matsengrp/phip-flow. The phippery library: https://github.com/matsengrp/phippery. The phip-viz Streamlit application: https://github.com/matsengrp/phip-viz.

Figure 1.

(A) The processing of sequencing data from a PhIP-Seq experiment begins with the alignment pipeline, which generates either a CSV file or xarray object containing the peptide counts across samples and associated annotations. (B) Custom analysis is performed with phippery library function calls, for example via the command line interface, and (C) visualization of results can be presented in an interactive manner using our Streamlit app.