LoRTIA – The Long-read RNA-Seq Transcript Isoform Annotator Toolkit
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The genetic information is first expressed during transcription. Transcripts carry the blueprints for protein synthesis, but transcripts can also regulate protein synthesis or even transcription itself. Knowing the transcriptional repertoire of an organism is crucial to the understanding of its molecular biology. Long-read sequencing, especially Nanopore sequencing has greatly furthered the field of transcriptomics. Previously, transcript models had to be assembled from short-read sequencing data, now, long-read sequencing is capable of capturing full-length transcripts. While transcript discovery based on long-read sequencing is more straight-forward compared to short-read sequencing, RNA fragmentation, RNA degradation and library preparation artefacts still complicate long-read transcriptome analysis. Available transcript annotation tools rely heavily on existing annotations and are likely to label fragmented reads or technical artefacts as full-length transcripts.