Genome-scale algorithmics (GSA)
Traphlor -- Transcript Prediction with Long Reads
Through transcription and alternative splicing, a gene can be transcribed into different RNA sequences (isoforms). The development of third-generation sequencers allowed for sequencing of reads up to several kilobases long. Compared to the short next-generation sequencing reads, which generally only span two exons at most, long reads can give additional information about which non-neighboring exons are part of which transcript.
Traphlor is a novel transcript prediction tool that utilizes the connectivity information gained from long reads spanning more than two exons. It is based on the idea of modeling long reads as subpath constraints, presented in the article "On the complexity of Minimum Path Cover with Subpath Constraints for multi-assembly" by Rizzi et al.
- Download the latest version here.
- The simulated data and scripts used in our experiments are available here.
For any questions, please contact us: aekuosma[at]cs.helsinki.fi