Abstract
We recently proposed a novel clone-by-clone protocol for de novo genome sequencing that leverages combinatorial pooling design to overcome the limitations of DNA barcoding when multiplexing a large number of samples on second-generation sequencing instruments. Here we address the problem of correcting the short reads obtained from our sequencing protocol. We introduce a novel algorithm called Scrible that exploits properties of the pooling design to accurately identify/correct sequencing errors and minimize the chance of “over-correcting”. Experimental results on synthetic data on the rice genome demonstrate that our method has much higher accuracy in correcting short reads compared to state-of-the-art error-correcting methods. On real data on the barley genome we show that Scrible significantly improves the decoding accuracy of short reads to individual BACs.
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Duma, D., Cordero, F., Beccuti, M., Ciardo, G., Close, T.J., Lonardi, S. (2015). Scrible: Ultra-Accurate Error-Correction of Pooled Sequenced Reads. In: Pop, M., Touzet, H. (eds) Algorithms in Bioinformatics. WABI 2015. Lecture Notes in Computer Science(), vol 9289. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-48221-6_12
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DOI: https://doi.org/10.1007/978-3-662-48221-6_12
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