A team from Australia, Spain, and Portugal has come up with a reference-free "greedy clustering" algorithm called RATTLE for putting together and quantifying transcript data based on Nanopore sequencing reads. As they report in the journal Genome Biology, the researchers applied RATTLE to simulated and real RNA sequence data on a variety of sample types, including human tissue samples. "Using simulated data, isoform spike-ins, and sequencing data from human tissues and cell lines, we show that RATTLE is competitive at recovering transcript sequences and their abundance, despite not using any information from the reference," the authors write, adding that their RATTLE method "lays the foundation for a multitude of potential new applications of Nanopore transcriptomics."
In Genome Biology, Researchers Share Algorithm for Reference-Free Nanopore-Based Transcript Analyses
Jul 11, 2022