1. A method of determining at least part of a genome of an organism from one or more samples, the one or more samples including nucleic acid molecules of the organism, the method comprising: receiving sequencing information of a plurality of the nucleic acid molecules in the one or more samples; identifying a plurality of candidate hets of a first chromosome, a candidate het being a locus identified as having or potentially having two or more different alleles; for each candidate het, a computing system determining whether the candidate het connects with each of a plurality of other candidate hets based on the sequencing information, wherein each connection specifies a first heterozygous locus having two alleles that connect respectively with two alleles of a second heterozygous locus; for each connection: determining an orientation between the pair of heterozygous loci of the connection, the orientation specifying which allele of the first heterozygous locus is connected with a first allele of the second heterozygous locus; and identifying a first set of at least ten heterozygous loci that are interconnected, the first set of heterozygous loci defining a first region of the first chromosome; and calculating two haplotypes of the first region based on the alleles of each heterozygous locus in the first set and the orientations of the connections among the heterozygous loci in the first set.