Estimation of Error Rates in Next Generation Sequencer: Analysis of Data Generated on the Roche(454) GS FLX Sequencer

Ali, Syed Zeeshan (2012) Estimation of Error Rates in Next Generation Sequencer: Analysis of Data Generated on the Roche(454) GS FLX Sequencer. Masters thesis, Indian Institute of Science Education and Research Kolkata.

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Abstract

When error rate and pattern are not investigated, a large number of reported polymorphisms may turn out to be false positives and resolution between low frequency alleles and artifacts can become difficult. In this study we have shown that error rates in 454 GS FLX are distributed non-randomly with high accumulation of error towards the end of longer reads which might convolute the data more than that is expected when only overall error rate is considered. The reason for this end-error is not clear and needs further in-depth study of the factors affecting sequencing and analysis of read-data. These results are specific to 454 GS FLX platform and may not be generalized to other NGS platforms. Therefore, routine checking of error pattern should and estimation of error rates should be a standard practice in NGS sequencing.

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