September 22, 2019  |  

Extensive and deep sequencing of the Venter/HuRef genome for developing and benchmarking genome analysis tools.

Authors: Zhou, Bo and Arthur, Joseph G and Ho, Steve S and Pattni, Reenal and Huang, Yiling and Wong, Wing H and Urban, Alexander E

We produced an extensive collection of deep re-sequencing datasets for the Venter/HuRef genome using the Illumina massively-parallel DNA sequencing platform. The original Venter genome sequence is a very-high quality phased assembly based on Sanger sequencing. Therefore, researchers developing novel computational tools for the analysis of human genome sequence variation for the dominant Illumina sequencing technology can test and hone their algorithms by making variant calls from these Venter/HuRef datasets and then immediately confirm the detected variants in the Sanger assembly, freeing them of the need for further experimental validation. This process also applies to implementing and benchmarking existing genome analysis pipelines. We prepared and sequenced 200?bp and 350?bp short-insert whole-genome sequencing libraries (sequenced to 100x and 40x genomic coverages respectively) as well as 2?kb, 5?kb, and 12?kb mate-pair libraries (49x, 122x, and 145x physical coverages respectively). Lastly, we produced a linked-read library (128x physical coverage) from which we also performed haplotype phasing.

Journal: Scientific data
DOI: 10.1038/sdata.2018.261
Year: 2018

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