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 this manuscript was in preparation, ONT released a new DNA basecalling strategy based on Flip-flop models. Flip-flop model basecalling screens the raw signal by comparing probabilities to either stay in the same nucleotide state or change to a new state. Additionally, the raw data is read by averaging over two sample points, as opposed to averaging over five sample points in standard model basecalling. These improvements have been shown to result in higher quality basecalling, and more importantly to increase the basecall fidelity over homopolymer sequences [35] . F I G U R E 2 | Workflow and performance of tailfindr on ONT DNA sequencing data 2A Schematic representation of Oxford Nanopore DNA Sequencing. In cDNA approaches, amplification is ensured by oligo-dT-aided anchoring of the End Primer (EP, blue) and addition of Front Primer sequence (FP, green) by strand-switch during reverse transcription. The Motor protein (red) is attached to the double-stranded DNA molecules at both ends by T4 DNA ligation. The Front Adapter (FA) bears the motor protein, while the End Adapter (EA) is a short complementary oligo that will ultimately appear at the 3'-end of resulting sequences. Both DNA strands will be sequenced from 5' to 3'. Thus, oligo-dT stretches will be present at the beginning of raw data, while oligo-dA stretches appear at the end. 2B Schematic workflow for ONT DNA sequencing data processing by the tailfindr algorithm. . CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . https://doi.org/10.1101/588343 doi: bioRxiv preprint