Using doublet information in genome mapping and assembly

A computer product comprising a computer readable medium storing a plurality of instructions, that when executed on one or more processors of a computer system, perform:

• receiving sequence data from a sequencing of a plurality of heteropolymer fragments corresponding to a heteropolymer molecule of an organism, wherein the sequence data for each heteropolymer fragment of the plurality of heteropolymer fragments includes:
• intensity values for monomers at a plurality of positions of the heteropolymer fragment;
• determining a first score of a first monomer at a first position of a first heteropolymer fragment based on a first intensity value of the first monomer measured at the first position, the first score providing a first likelihood of the first monomer being at the first position of the first heteropolymer fragment;
• determining a second score of a second monomer at the first position of the first heteropolymer fragment based on a second intensity value of the second monomer measured at the first position, the second score providing a second likelihood of the second monomer being at the first position of the first heteropolymer fragment;
• based on the first score and the second score, identifying the first position of the first heteropolymer fragment to correspond to a multiplet call that includes the first monomer and the second monomer;
• and
• using the first monomer and the second monomer in a mapping procedure and/or an assembly procedure to determine a final monomer call at a final position in a sequence of monomers corresponding to the heteropolymer molecule of the organism.