VIsoQLR: an interactive tool for the detection, quantification and fine-tuning of isoforms using long-read sequencing

Abstract

DNA variants altering the pre-mRNA splicing process represent an underestimated cause of human genetic diseases. Their association with disease traits should be confirmed using functional assays from patient cell lines or other alternative models to detect the formation of aberrant mRNAs. Long-read sequencing is a suitable technique to identify and quantify mRNA isoforms. Available isoform clusterization and/or quantification tools are generally designed for the whole transcriptome analysis. Experiments focusing on a single locus analysis need more precise data fine-tuning and visualization tools. Here we describe VIsoQLR, an interactive analyzer, viewer and editor for the semi-automated identification and quantification of known and novel isoforms using long-read sequencing data. VIsoQLR is tailored to thoroughly analyze mRNA expression and maturation in low-throughput splicing assays. This tool takes sequences aligned to a reference, defines consensus splice sites, and quantifies isoforms. Users can edit splice sites through dynamic and interactive graphics and tables as part of their manual curation. Known transcripts, or isoforms detected by other methods, can also be imported as references for comparison. Here, we explain VIsoQLR principles and features, and show its applicability in a case study example using Nanopore sequencing. VIsoQLR is available at https://github.com/TBLabFJD/VIsoQLR.