Contiguity-Preserving Transposition Sequencing

CPT-seq is a method for genome-wide haplotyping based on contiguity-preserving transposition (CPT) and combinatorial indexing (Amini et al., 2014) . Tn5 transposition is used to modify DNA with adapter and index sequences while preserving contiguity. After DNA dilution and compartmentalization, the transposase is removed, and the DNA is separated into individually indexed libraries. The libraries in each compartment are enriched for neighboring genomic elements and are further indexed via PCR. Combinatorial 96-plex indexing at both the transposition and PCR stage enables the construction of phased synthetic reads from each of the nearly 10,000 virtual compartments.


  • Highly indexed and efficient
  • FragScaff reported to be highly effective at scaffolding large genomes from CPT-seq data (Kuleshov et al., 2016)
  • Large effective number of virtual compartments per physical compartment could avoid the amplification biases associated with multiple displacement amplification (MDA) Cao et al., 2016)


  • Not yet adopted widely by the scientific community


Illumina Library prep and Array Kit Selector


Mostovoy Y., Levy-Sakin M., Lam J., et al. A hybrid approach for de novo human genome sequence assembly and phasing. Nat Methods. 2016;13:587-590

Snyder M. W., Adey A., Kitzman J. O. and Shendure J. Haplotype-resolved genome sequencing: experimental methods and applications. Nat Rev Genet. 2015;16:344-358


Amini S., Pushkarev D., Christiansen L., et al. Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing. Nat Genet. 2014;46:1343-1349