PepSIRF + QIIME 2: software tools for automated, reproducible analysis of highly-multiplexed serology data

Abstract

PepSIRF is a command-line, module-based open-source software package that facilitates the analysis of data from highly-multiplexed serology assays (e.g., PepSeq or PhIP-Seq). It has nine separate modules in its current release (v1.5.0): demux, info, subjoin, norm, bin, zscore, enrich, link, and deconv. These modules can be used together to conduct analyses ranging from demultiplexing raw high-throughput sequencing data to the identification of enriched peptides. QIIME 2 is an open-source, community-developed and plugin-based bioinformatics platform that focuses on data and analytical transparency. QIIME 2's features include integrated and automatic tracking of data provenance, a semantic type system, and built-in support for many types of user interfaces. Here, we describe three new QIIME 2 plugins that allow users to conduct PepSIRF analyses within the QIIME 2 environment and extend the core functionality of PepSIRF in two key ways: 1) enabling generation of interactive visualizations and 2) enabling automation of analysis pipelines that include multiple PepSIRF modules.