Title :
Optimal DNA shotgun sequencing: Noisy reads are as good as noiseless reads
Author :
Motahari, Amin ; Ramchandran, Kannan ; Tse, David ; Nan Ma
Author_Institution :
Dept. of Electr. Eng. & Comput. Sci., Univ. of California, Berkeley, Berkeley, CA, USA
Abstract :
We establish the fundamental limits of DNA shotgun sequencing under noisy reads. We show a surprising result: for the i.i.d. DNA model, noisy reads are as good as noiseless reads, provided that the noise level is below a certain threshold which can be surprisingly high. As an example, for a uniformly distributed DNA sequence and a symmetric substitution noisy read channel, the threshold is as high as 19%.
Keywords :
DNA; genomics; DNA model; noiseless reads; noisy reads; optimal DNA shotgun sequencing; Assembly; DNA; Greedy algorithms; Noise; Noise level; Noise measurement; Sequential analysis;
Conference_Titel :
Information Theory Proceedings (ISIT), 2013 IEEE International Symposium on
Conference_Location :
Istanbul
DOI :
10.1109/ISIT.2013.6620505