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Data released on December 12, 2012

Updated genome assembly of YH: the first diploid genome sequence of a Han Chinese individual (version 2, 07/2012)

Fang, X; Li, Y; Li, Z; Liu, B; Luo, R; Wang, J; Xie, Y; Zheng, H; Qin, J; Yang, B; Yu, C; Ni, P; Li, N; Guo, G; Ye, J; Fang, L; Su, Y; Asan, ; Zheng, H; Kristiansen, K; Wong, G, K; Nielsen, R; Durbin, R; Bolund, L; Zhang, X; Li, S; Yang, H; Wang, J (2012): Updated genome assembly of YH: the first diploid genome sequence of a Han Chinese individual (version 2, 07/2012) GigaScience Database. http://dx.doi.org/10.5524/100038 RIS BibTeX Text

Updated genomic data from the YH (Homo sapiens) diploid genome – the first sequenced Han Chinese individual, a representative of the Asian population. The genomic DNA used in this study came from an anonymous male Han Chinese individual who has no known genetic diseases. The original version of the YH genome was assembled based on 3.3 billion reads using the Illumina Genome Analyzer (see dataset doi:10.5524/100015). This latest (as of 07/2012) and improved version of the YH genome was assembled based on 2.1 billion reads using the Illumina HiSeq2000. A total of 202G nucleotides data was achieved using 100 bp-long paired end reads with an insert size ranging from 180 bp to 40 kbp, and the genome was sequenced to 67.5-fold average coverage. The latest version of SOAPdenovo2 was used to reassemble, improve and update the previously assembled genome (tools and pipelines available here: doi:10.5524/100044). By aligning the short reads with SOAP, 177G nucleotides were mapped onto the NCBI reference genome and 99.99% of the genome was covered. The raw sequences, assemblies and relevant tools are released for public use under a CC0 license. More information about the YH genome can be viewed at: http://yh.genomics.org.cn/

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Related manuscripts:

doi:10.1038/nature07484 (PubMed: 18987735)

Related datasets:

doi:10.5524/100038 IsNewVersionOf doi:10.5524/100015
doi:10.5524/100038 IsCompiledBy doi:10.5524/100044
doi:10.5524/100038 IsSupplementedBy doi:10.5524/100097
doi:10.5524/100038 IsSupplementedBy doi:10.5524/100096

Additional information:

http://yh.genomics.org.cn/

Genome browser:

http://yh.genomics.org.cn/mapview.jsp?

Accessions (data included in GigaDB):

ENA: ERP001652

Projects:


Genomic

http://gigadb.org/images/data/cropped/100013_YH.jpg

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
YH9606HumanhumanHomo sapiens
Displaying 1-1 of 1 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
YHGenome sequenceFASTQ5.96 GB2012-12-12
YHGenome sequenceFASTQ5.32 GB2012-12-12
YHGenome sequenceFASTQ5.16 GB2012-12-12
YHGenome sequenceFASTQ5.06 GB2012-12-12
YHGenome sequenceFASTQ4.86 GB2012-12-12
YHGenome sequenceFASTQ6.49 GB2012-12-12
YHGenome sequenceFASTQ6.14 GB2012-12-12
YHGenome sequenceFASTQ6.48 GB2012-12-12
YHGenome sequenceFASTQ6.11 GB2012-12-12
YHGenome sequenceFASTQ5.15 GB2012-12-12
Displaying 1-10 of 15 File(s).

History:

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