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Sci Data. 2018 Dec 18;5:180261. doi: 10.1038/sdata.2018.261.

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

Author information

1
Department of Psychiatry and Behavioral Sciences, Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.
2
Department of Statistics, Department of Biomedical Data Science, Bio-X Program, Stanford University, Stanford, California 94305, USA.
3
Tashia and John Morgridge Faculty Scholar, Stanford Child Health Research Institute, Palo Alto, California 94305, USA.

Abstract

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.

PMID:
30561434
PMCID:
PMC6298255
DOI:
10.1038/sdata.2018.261
[Indexed for MEDLINE]
Free PMC Article

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