In vitro, long-range sequence information for de novo genome assembly via transposase contiguity

Andrew Adey, Jacob O. Kitzman, Joshua N. Burton, Riza Daza, Akash Kumar, Lena Christiansen, Mostafa Ronaghi, Sasan Amini, Kevin L. Gunderson, Frank J. Steemers, Jay Shendure

Research output: Contribution to journalArticlepeer-review

112 Scopus citations


We describe a method that exploits contiguity preserving transposase sequencing (CPT-seq) to facilitate the scaffolding of de novo genome assemblies. CPT-seq is an entirely in vitro means of generating libraries comprised of 9216 indexed pools, each of which contains thousands of sparsely sequenced long fragments ranging from 5 kilobases to >1 megabase. These pools are "subhaploid," in that the lengths of fragments contained in each pool sums to ∼5% to 10% of the full genome. The scaffolding approach described here, termed fragScaff, leverages coincidences between the content of different pools as a source of contiguity information. Specifically, CPT-seq data is mapped to a de novo genome assembly, followed by the identification of pairs of contigs or scaffolds whose ends disproportionately co-occur in the same indexed pools, consistent with true adjacency in the genome. Such candidate "joins" are used to construct a graph, which is then resolved by a minimum spanning tree. As a proof-of-concept, we apply CPT-seq and fragScaff to substantially boost the contiguity of de novo assemblies of the human, mouse, and fly genomes, increasing the scaffold N50 of de novo assemblies by eight- to 57-fold with high accuracy. We also demonstrate that fragScaff is complementary to Hi-C-based contact probability maps, providing midrange contiguity to support robust, accurate chromosome-scale de novo genome assemblies without the need for laborious in vivo cloning steps. Finally, we demonstrate CPT-seq as a means of anchoring unplaced novel human contigs to the reference genome as well as for detecting misassembled sequences.

Original languageEnglish (US)
Pages (from-to)2041-2049
Number of pages9
JournalGenome Research
Issue number12
StatePublished - Dec 1 2014

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)


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