IRIS: an accurate and efficient barcode calling tool for in situ sequencing

Abstract

SummaryThe emerging in situ RNA sequencing technologies which can capture and amplify RNA within the original tissues provides efficient solution for producing spatial expression map from dozens to thousands of genes. Most of in situ RNA-seq strategies developed recently infer the expression patterns based on the fluorescence signals from the images taken during sequencing. However, an automate and convenient tool for decoding signals from image information is still absent. Here we present an easy-to-use software named IRIS to efficiently decode image signals from in situ sequencing into nucleotide sequences. This software can record the quality score and the spatial information of the sequencing signals. We also develop an interactive R shiny app named DAIBC for data visualization. IRIS is designed in modules so that it could be easily extended and compatible to new technologies. Availability and implementationIRIS and DAIBC are freely available under BSD 3-Clause License at: https://github.com/th00516/ISS_pyIRIS. Contactguojie.zhang@bio.ku.dk