Error correction and DeNovo genome Assembly for the MinIon sequencing reads mixing Illumina short reads

The new MinIon sequencer provided by the Oxford Nanopore Technologies is characterized by his small size and is powered from the USB 3.0 port of a laptop computer. 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 (about 25% [1]) 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 pipeline that detects and corrects errors for MinIon long reads using preassembled Illumina MiSeq short reads and we use the Overlap-Layout-Consensus(OLC) approach to assemble the corrected reads. MiRCA is able to correct: deletions, insertions and substitutions errors by forming a multiple sequence alignment and does not require a large memory space. We use the Saccharomyces cerevisiae W303 genome and the Escherichia coli K-12 MG1655 bacterial genome to test the efficiency of our pipeline.