Coded Shotgun Sequencing
Most DNA sequencing technologies are based on the shotgun paradigm: many short reads are obtained from random unknown locations in the DNA sequence. A fundamental question, in Motahari et al., (2013), is what read length and coverage depth (i.e., the total number of reads) are needed to guarantee reliable sequence reconstruction. Motivated by DNA-based storage, we study the coded version of this problem; i.e., the scenario where the DNA molecule being sequenced is a codeword from a predefined codebook.