LongPolyASE: An end-to-end framework for allele-specific gene and isoform analysis in polyploids using long-read RNA-seq

MotivationLong-read RNA-seq and phased reference genomes enable haplotype-resolved gene and isoform expression analysis. While methods and tools exist for diploid organisms, analysis tools for polyploids are lacking. ResultsWe developed an end-to-end framework for allele-specific gene and isoform analysis in polyploids with three components: Syntelogfinder identifies syntenic genes in phased assemblies; longrnaseq quantifies transcripts, discovers novel isoforms, and performs quality control of long-read RNA-seq; and PolyASE analyzes differential allelic expression, differential isoform usage between conditions, and structural differences in major isoforms between haplotypes. We demonstrate the use of the framework on diploid rice and autotetraploid potato. Availability and ImplementationSyntelogfinder and longrnaseq are implemented in Nextflow and available on GitHub. PolyASE is a Python package available on PyPI. The framework is fully documented and tutorials are provided. ContactNadja.nolte.franziska@nib.si Supplementary informationSupplementary data are available online and on Zenodo.