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PepSIRF is a command-line, module-based open-source software package thatfacilitates 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 fromdemultiplexing raw high-throughput sequencing data to the identification ofenriched peptides. QIIME 2 is an open-source, community-developed andplugin-based bioinformatics platform that focuses on data and analyticaltransparency. QIIME 2's features include integrated and automatic tracking ofdata provenance, a semantic type system, and built-in support for many types ofuser interfaces. Here, we describe three new QIIME 2 plugins that allow usersto conduct PepSIRF analyses within the QIIME 2 environment and extend the corefunctionality of PepSIRF in two key ways: 1) enabling generation of interactivevisualizations and 2) enabling automation of analysis pipelines that includemultiple PepSIRF modules.

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