nf-core/isoseq: simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing.

ABSTRACT

MOTIVATION Iso-Seq RNA long-read sequencing enables the identification of full-length transcripts and isoforms, removing the need for complex analysis such as transcriptome assembly. However, the raw sequencing data need to be processed in a series of steps before annotation is complete. Here, we present nf-core/isoseq, a pipeline for automatic read processing and genome annotation. Following nf-core guidelines, the pipeline has few dependencies and can be run on any of platforms. AVAILABILITY AND IMPLEMENTATION The pipeline is freely available online on the nf-core website (https//nf-co.re/isoseq) and on GitHub (https//github.com/nf-core/isoseq) under MIT License (DOI 10.5281/zenodo.7116979).