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bioRxiv · 10.1101/2021.12.17.457386

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

Le, D. D.·Orcales, F. T.·Stephenson, W.
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Abstract

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.

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Le, D. D., Orcales, F. T., Stephenson, W.. 2021-12-20. isoformant: A visual toolkit for reference-free long-read isoform analysis at single-read resolution. https://doi.org/10.1101/2021.12.17.457386

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