CPT-Seq

CPT-Seq

Genome-wide haplotyping based on contiguity-preserving transposition (CPT-seq) and combinatorial indexing. Tn5 transposition is used to modify DNA with adaptor and index sequences while preserving contiguity. After DNA dilution and compartmentalization, the transposase is removed and the DNA 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.

Pros:

• Highly indexed and efficient
• FragScaff to be highly effective at scaffolding large genomes from CPT-seq data¹
• The large effective number of virtual compartments per physical compartment could avoid the amplification biases associated with MDA²

Cons:

• The method has not been adopted widely

• CPT-Seq: Amini S., Pushkarev D., Christiansen L., Kostem E., Royce T., et al. (2014) Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing. Nat Genet 46: 1343-1349
• 1. Kuleshov V., Snyder M. P. and Batzoglou S. (2016) Genome assembly from synthetic long read clouds. Bioinformatics 32: i216-i224
• 2. Cao C.-c. and Sun X. (2016) Combinatorial pooled sequencing: experiment design and decoding. Quantitative Biology 4: 36-46

1. Amini S., Pushkarev D., Christiansen L., Kostem E., Royce T., et al. (2014) Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing. Nat Genet 46: 1343-1349
2. Mostovoy Y., Levy-Sakin M., Lam J., Lam E. T., Hastie A. R., et al. (2016) A hybrid approach for de novo human genome sequence assembly and phasing. Nat Methods 13: 587-590
3. Snyder M. W., Adey A., Kitzman J. O. and Shendure J. (2015) Haplotype-resolved genome sequencing: experimental methods and applications. Nat Rev Genet 16: 344-358