To support long-read RNA-seq analysis, MDL has built an online resource for bulk and single-cell RNA isoform sequencing analysis. We hope this resource will serve as a useful guide for this feature rich data type. Computational tools can be found on our MDL github.
Software:
LongReadAlignmentAssembler (LRAA) - a tool designed for isoform discovery and/or quantification from long read RNA-Seq data, specifically utilized for MAS-Iso-Seq isoform identification
Integrative Transcriptomics Viewer (ITV) - a Python package based on a fork of Genomeview designed to visualize long-read sequencing data in a transcriptomic context and facilitate interactive comparisons
CTAT-LR-Fusion - a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT) designed to detect fusion transcripts from long-read transcriptome sequencing data (including PacBio Iso-seq and Oxford Nanopore), with the ability to leverage matched Illumina short reads for integrated exploration and quantification
marti - a lightweight framework for the classification and quantification of artefactual long-read cDNA constructs