  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.
