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Ivan de la Rubia

Reference-free reconstruction and quantification of transcriptomes from nanopore long-read sequencing

About Ivan de la Rubia

Ivan de la Rubia is a Ph.D. student in Eyras’ group at the John Curtin School of Medical Research (JCSMR - ANU) and carries out his work at the Biomedical Informatics Program of the Pompeu Fabra University (UPF) / Hospital del Mar Research Institute. In 2015, he graduated in Computer Science at the Polytechnical University of Catalonia (UPC), specializing in the area of algorithms and data structures. From 2015 to 2017, he worked at the Data Management Group at UPC (DAMA-UPC). In 2016 he enrolled into the MSc in Bioinformatics for Health of the UPF.


We have developed RATTLE, a new method for the reference-free reconstruction of transcriptomes from nanopore sequencing reads. RATTLE uses a new k-mer based similarity measure to cluster reads and quantify transcripts, perform error correction, and delineate alternative transcript isoforms from long reads without the need of a genome reference. Using experimental and simulated data, we show that RATTLE outperforms other methods at clustering, and it achieves a detection of known splice-sites similar to reference-based methods. RATTLE enables the improved characterization of transcriptomes operating in cells across multiple conditions and disease states directly from long-read sequencing, opening up the application of quantitative transcriptomics in cell models, non-model organisms, and individuals for which a genome reference is not available. Our method, together with the mobility of nanopore technology, will facilitate the systematic implementation of long-read transcriptomics in clinical and field work.

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Ivan de la Rubia

Ivan de la Rubia