Abstract
The new generation of long reads generated by Oxford nanopore sequencing technology has revolutionized the next generation sequencing environment with the appearance of its new sequencer MinIon. This sequencer produces long reads with a low production costs and with high throughput. However, long reads generated by the MinIon sequencer have a high error rate which deteriorates the quality of results obtained by analyzing these long reads. A solution to correct long reads is to use the high coverage and the high quality of short reads generated by the second generation sequencing technology. Here, we present MiRCA (MinIon Reads Correction Algorithm) a hybrid approach based on the sequences alignments that detects and corrects errors for MinIon long reads using preassembled Illumina short reads. With this new error correction approach, we were able to make an effective and quick de novo assembly. Experiments on Saccharomyces cerevisia and the Escherichia coli genomes show that MiRCA is much better than the available tools. MiRCA is tested on Linux platforms and freely available at https://github.com/Mkchouk/MiRCA.