Alladi Ramakrishnan Hall

Ultra long DNA sequence reads from the mobile nanopore sequencers: computational challenges in error correction, assembly and alignment

Raja Mugasimangalam

Genotypic Technology, Bengaluru

Nanopore sequencer is a portable handheld sequencer that is making waves in the genomics community - The low cost sequencer is democratizing genomics and the taking the sequencing from core labs to every one. The Nanopore sequencer operates by the principle of voltage disturbance that occurs when a DNA strand passes through a Protein Nanopore. The electrical disturbance is captured in the form of "squiggle file" also called as FAST5 file format. This FAST5 file is converted to DNA sequence text file using base caller software which is trained using standards of known DNA sequences. The data generated is extremely long > 150 Kilo bases and readily solved the problem of sequence similarity searches. However the error rate of a Nanopore sequence read is as high as 10%. Algorithms have been developed by various groups to reduce the error rate, but the 10% error rate still remains. The errors are random and not systematic, however, there enough scope for theoretical computer scientists to model the error and develop algorithms to correct the error. Even marginal improvements in accuracy OR differentiating erroneous calls from accurate calls can make a big difference in down stream sequence analysis processes of assembly and alignment.

During my presentation, I will run the Nanopore sequencer and share the sequence data. I will also bring DNA sequence data sets generated by Nanopore and the corresponding correct DNA sequences.