isoformant: A visual toolkit for reference-free long-read isoform analysis at single-read resolution

isoformant is an analytical toolkit for isoform characterization of Oxford Nanopore Technologies (ONT) long-transcript sequencing data (i.e. direct RNA and cDNA). Deployment of these tools using Jupyter Notebook enables interactive analysis of user-defined region-of-interest (ROI), typically a gene. The core module of isoformant clusters sequencing reads by k-mer density to generate isoform consensus sequences without the requirement for a reference genome or prior annotations. The inclusion of differential isoform usage hypothesis testing based on read distribution among clusters enables comparison across multiple samples. Here, as proof-of-principle, we demonstrate the utility of isoformant for analyzing isoform diversity of commercially-available isoform standard mixtures. isoformant is available here: https://github.com/danledinh/isoformant.