tailfindr: Alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing

Maximilian Krause; Adnan M. Niazi; Kornel Labun; Yamila N. Torres Cleuren; Florian S. Müller; Eivind Valen

While not being as precise in measuring poly(A) tails, ONT long-read sequencing approaches have unique advantages over short-read sequencing approaches. First, ONT sequencing is intrinsically a single-molecule technique. Second, RNA sequencing approaches are amplification-free, avoiding the emergence of possible amplification artefacts. Third, since the native molecule is sequenced as it comes from the specimen, additional features of the RNA can measured directly, as was shown for RNA modifications [32, 40] . Fourth, and most importantly, long-read sequencing allows direct assignment of transcript isoforms to single molecules without bioinformatics post-processing, making truly isoform-specific measurements of poly(A) tail lengths possible. Additionally, ONT sequencing allows to study features of 5'-end and 3'-end events of the same molecule in conjunction with the poly(A) tail length. Together, ONT sequencing in conjunction with tailfindr poly(A) estimation offers great potential to combine the study of poly(A) tail length and other RNA features with transcript-isoform specificity in one assay.