A method of assembling short nucleic acid fragments of a target nucleic acid, wherein the target nucleic acid has a region of interest for interrogation, said method comprising the steps of: A. mixing said short nucleic acid fragments with an assembler sequence, wherein said assembler sequence is longer than each of said short nucleic acid fragments, said assembler sequence is derived from the same genetic species as said target nucleic acid and said assembler sequence is substantially complementary to said target nucleic acid, and said short nucleic acid fragments contain one or more SNVs compared with said assembler sequence; B. annealing said short nucleic acid fragments to said assembler sequence and extending said short nucleic acid fragments in the 3'-direction by polymerase to produce a collection of first duplex nucleic acids containing a collection of first nucleic acids and said assembler sequence; C. disassociating said assembler sequence from said collection of first nucleic acids; D. annealing a primer to said collection of first nucleic acids wherein said primer has a sequence the same as a region of the assembler sequence that is 5' to the region of interest for interrogation of the target nucleic acid, and extending said primer in the 3'-direction with polymerase to produce a collection of second duplex nucleic acids containing a collection of second nucleic acids and said collection of first nucleic acids; E. dissociating said collections of said first and said second nucleic acids; F. annealing said collections of first and second nucleic acids with one another and said assembler sequence and extending said collection of said first and said second nucleic acids in the 3' direction; and G. repeating steps E and F, thereby amplifying said target nucleic acid. A. mixing said short nucleic acid fragments with an assembler sequence, wherein said assembler sequence is longer than each of said short nucleic acid fragments, said assembler sequence is derived from the same genetic species as said target nucleic acid and said assembler sequence is substantially complementary to said target nucleic acid, and said short nucleic acid fragments contain one or more SNVs compared with said assembler sequence; B. annealing said short nucleic acid fragments to said assembler sequence and extending said short nucleic acid fragments in the 3'-direction by polymerase to produce a collection of first duplex nucleic acids containing a collection of first nucleic acids and said assembler sequence; C. disassociating said assembler sequence from said collection of first nucleic acids; D. annealing a primer to said collection of first nucleic acids wherein said primer has a sequence the same as a region of the assembler sequence that is 5' to the region of interest for interrogation of the target nucleic acid, and extending said primer in the 3'-direction with polymerase to produce a collection of second duplex nucleic acids containing a collection of second nucleic acids and said collection of first nucleic acids; E. dissociating said collections of said first and said second nucleic acids; F. annealing said collections of first and second nucleic acids with one another and said assembler sequence and extending said collection of said first and said second nucleic acids in the 3' direction; and G. repeating steps E and F, thereby amplifying said target nucleic acid.