High-coverage, long-read sequencing of Han Chinese trio reference samples

Ying-Chih Wang; Nathan D Olson; Gintaras Deikus; Hardik Shah; Aaron M Wenger; Jonathan Trow; Chunlin Xiao; Stephen Sherry; Marc L Salit; Justin M Zook; Melissa Smith; Robert Sebra

doi:10.1038/s41597-019-0098-2

High-coverage, long-read sequencing of Han Chinese trio reference samples

Sci Data. 2019 Jun 14;6(1):91. doi: 10.1038/s41597-019-0098-2.

Authors

Ying-Chih Wang¹, Nathan D Olson², Gintaras Deikus¹, Hardik Shah¹, Aaron M Wenger³, Jonathan Trow⁴, Chunlin Xiao⁴, Stephen Sherry⁴, Marc L Salit⁵, Justin M Zook⁶, Melissa Smith^{1

7}, Robert Sebra^{1

7}

Affiliations

¹ Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L Levy Pl, New York, NY, 10029, USA.
² Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr, MS8312, Gaithersburg, MD, 20899, USA. [email protected].
³ Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA, 94025, USA.
⁴ National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD, 20894, USA.
⁵ Joint Initiative for Metrology in Biology, Stanford, CA, 94305, USA.
⁶ Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr, MS8312, Gaithersburg, MD, 20899, USA. [email protected].
⁷ Icahn Institute of Data Science and Genomic Technology, 1 Gustave L Levy Pl, New York, NY, 10029, USA.

Abstract

Single-molecule long-read sequencing datasets were generated for a son-father-mother trio of Han Chinese descent that is part of the Genome in a Bottle (GIAB) consortium portfolio. The dataset was generated using the Pacific Biosciences Sequel System. The son and each parent were sequenced to an average coverage of 60 and 30, respectively, with N50 subread lengths between 16 and 18 kb. Raw reads and reads aligned to both the GRCh37 and GRCh38 are available at the NCBI GIAB ftp site (ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/ChineseTrio/). The GRCh38 aligned read data are archived in NCBI SRA (SRX4739017, SRX4739121, and SRX4739122). This dataset is available for anyone to develop and evaluate long-read bioinformatics methods.

Publication types

Dataset
Research Support, N.I.H., Intramural

MeSH terms

Asian People / genetics*
China
Databases, Genetic*
Female
Genome, Human*
High-Throughput Nucleotide Sequencing
Humans
Male
Nuclear Family*
Sequence Analysis, DNA