  By coupling peptides with DNA tags (i.e., 'barcodes'), it is now possible to
harness high-throughput sequencing (HTS) technologies to enable highly
multiplexed peptide-based assays, which have a variety of potential
applications including broad characterization of the epitopes recognized by
antibodies. While the processing of HTS data, in general, is already well
supported, there are very few software tools that have been developed for
working with data generated in these highly-multiplexed peptide assays. In
order to fill this gap, we present PepSIRF (Peptide-based Serological Immune
Response Framework), which is a flexible and comprehensive software package
designed specifically for the analysis of HTS data from highly-multiplexed
peptide-based assays.
