Disclosed herein are methods, compositions, and systems that utilize the consensus sequencing of rolling circle amplified short templates. Methods of determining a nucleic acid sequence can include one or more steps of contacting a nucleic acid in a sample to an endonuclease to cleave a target nucleic acid; ligating the target nucleic acid sequence to form a circular target nucleic acid; hybridizing at least one primer to the circular target molecule to form amplified nucleic acid through rolling circle amplification; and performing sequence analysis of the amplified nucleic acid.