Described herein are inexpensive high throughput methods to convert a target single stranded DNA (ssDNA) such that each nucleotide (or base) adenine (A), thymine (T), guanine (G) and cytosine (C) is converted to a pre-determined oligonucleotide code, with the sequential order preserved in the converted ssDNA, or RNA. The method does not require the use of DNA polymerases during the cycles and involves the use of an oligonucleotide probe library with repeated cycles of ligation and cleavage. At each cycle, one or more nucleotides on one end (e.g., either the 5' end or the 3' end) of a target, e.g ssDNA, are cleaved and then ligated with the corresponding oligonucleotide code at the other end of the target ssDNA.