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

被引:127
作者
Adey, Andrew [1 ]
Kitzman, Jacob O. [1 ]
Burton, Joshua N. [1 ]
Daza, Riza [1 ]
Kumar, Akash [1 ]
Christiansen, Lena [2 ]
Ronaghi, Mostafa [2 ]
Amini, Sasan [2 ]
Gunderson, Kevin L. [2 ]
Steemers, Frank J. [2 ]
Shendure, Jay [1 ]
机构
[1] Univ Washington, Dept Genome Sci, Seattle, WA 98115 USA
[2] Illumina Inc, Adv Res Grp, San Diego, CA 92122 USA
基金
美国国家科学基金会;
关键词
LOW-INPUT; CONSTRUCTION; CHROMATIN; DATABASE; READS;
D O I
10.1101/gr.178319.114
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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 similar 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.
引用
收藏
页码:2041 / 2049
页数:9
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