Most genomes to date have been sequenced without taking into account the diploid 
nature of the genome. However, the distribution of variants on each individual 
chromosome can (1) significantly impact gene regulation and protein function, 
(2) have important implications for analyses of population history and medical 
genetics, and (3) be of great value for accurate interpretation of medically 
relevant genetic variation. Here, we describe a comprehensive and detailed 
protocol for an ultra fast (<3 h library preparation), cost-effective, and 
scalable haplotyping method, named Contiguity Preserving Transposition 
sequencing or CPT-seq (Amini et al., Nat Genet 46(12):1343-1349, 2014). CPT-seq 
accurately phases >95 % of the whole human genome in Mb-scale phasing blocks. 
Additionally, the same workflow can be used to aid de novo assembly (Adey et 
al., Genome Res 24(12):2041-2049, 2014), detect structural variants, and perform 
single cell ATAC-seq analysis (Cusanovich et al., Science 348(6237):910-914, 
2015).