Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing
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Long-read sequencing technologies still produce a considerable error rate, averaging around 10% in the case of ONT MinION. Full-length transcript sequencing in eukaryotes have the added challenge of having to deal with introns and small transcript variations (alternative splicing). This presents challenges not only for error correction but also for sequence alignment to reference genomes. We have thus developed RATTLE, a new method for the reference-free reconstruction of transcriptomes from long-read sequencing from Nanopore. RATTLE clusters long (cDNA and RNA) reads using approximate sequence similarity, performs error correction per cluster, and outputs corrected reads and quantified transcripts.