Data Sets

The sequencing data used for analyses on this website represent the latest publicly available data sets. All Illumina data generated internally can be downloaded from the appropriate subsection below. Data sets were contributed from original manuscripts or made available through company website. URLs to their online locations are listed below.

Illumina-Generated Data:
Description	Platform	File Type	Suitable Analysis¹	Download
Sequencing Runs
Chr 21 NA18507⁴	Illumina v3 cBOT chemistry HiSeq³	BAM	Q,C,V,FN	[Download]
Chr 19 NA18507⁴	Illumina v3 cBOT chemistry HiSeq³	BAM	Q,C,V,FN	[Download]
Chr 4 NA18507⁴	Illumina v3 cBOT chemistry HiSeq³	BAM	Q,C,V,FN	[Download]
Chr 21 NA19240²	Illumina GA IIx	BAM	Q,C,V,FN	[Download]
Chr 21 NA19240²	Illumina HiSeq	BAM	Q,C,V,FN	[Download]
Chr 21 NA18507²	Illumina GA IIx	BAM	Q,C,V,FN	[Download]
E. coli (MG1655) Read 1	Illumina GA IIx	BAM	Q,C	[Download]
E. coli (MG1655) Read 2	Illumina GA IIx	BAM	Q,C	[Download]
E. coli (MG1655) Paired	Illumina GA IIx	BAM	Q,C	[Download]
Variant Calls
NA18507 SNPs	Illumina GA IIx	TXT	T,FN	[Download]
NA18506 SNPs	Illumina GA IIx	TXT	T,FN	[Download]
NA18508 SNPs	Illumina GA IIx	TXT	T,FN	[Download]
NA19240 SNPs	Illumina GA IIx	TXT	FN	[Download]
NA19240 Indels	Illumina GA IIx	TXT	FN	[Download]
Coverage Output
NA19240 coverage²	Illumina GA IIx	TXT	G	[Download]

¹ Q = Quality Scores; C = Coverage; V = Variant Calling; T = Trio Inheritance; FN = False Negatives; G = Gene Region Gaps
² Chromosome 21. All human data were aligned to the b36/hg18 reference genome.
³ v3 cBOT Kit Chemistry, available Q2, 2011.
⁴ All data generated with v3 cBOT Kit Chemistry on HiSeq2000 and aligned to the b37/hg19 reference genome.

Externally Generated Data:
Description	Platform	File Type	Suitable Analysis¹	URL
Sequencing Runs
KB1 (Bushman)²	Illumina GA IIx	BAM	Q,C,V,FN	ftp://ftp.bx.psu.edu/data/bushman/hg18/bam/ as of 13-10-2010
ABT (Bantu)²	SBL (version 3)	BAM	Q,C,V,FN	ftp://ftp.bx.psu.edu/data/bushman/hg18/bam/ as of 13-10-2010
Human1 (NA18507)³	Illumina GA II	FASTQ	Q,C,V,FN	http://www.ncbi.nlm.nih.gov/sra/?term=SRA000271 as of 13-10-2010
E. coli (MG1655)	Illumina GA IIx	FASTQ	Q,C,	http://www.ebi.ac.uk/ena/data/view/ERP000092 as of 13-10-2010
E. coli (DH10B)	SBL (version 4)	CSFASTA; QUAL	Q,C	http://solidsoftwaretools.com/gf/project/dh10bfrag/ as of 13-10-2010
1000 Genomes⁴	Illumina, SBL	BAM	Q,C,V,T,FN	ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/data ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data as of 13-10-2010
Variant Calls
NA18507 SNPs	SBL (version 2)	TXT	FN	http://solidsoftwaretools.com/gf/project/yoruban as of 13-10-2010
NA18507 Indels	SBL (version 2)	TXT	FN	http://solidsoftwaretools.com/gf/project/yoruban as of 13-10-2010

¹ Q = Quality Scores; C = Coverage; V = Variant Calling; T = Trio Inheritance; FN = False Negatives
² Complete Khoisan and Bantu genomes from southern Africa. All human data were aligned to the b36/hg18 reference genome. (Schuster SC, et al. Nature. 2010 Feb 18; 463 (7283): 943-947)
³ Accurate whole human genome sequencing using reversible terminator chemistry. All human data were aligned to the b36/hg18 reference genome. (Bentley DR, et al. Nature. 2008 Nov 6; 456 (7218): 53-59)
⁴ 1000 Genomes files can be used by individuals for personal script assessment, but cannot be published or used for competitive purposes. Data from 1000 Genomes are aligned to the b37/hg19 reference genome.

Reference Files:
Description	File Type	Download
Reference Genomes
NCBI build 36	FASTA	http://hgdownload.cse.ucsc.edu/goldenPath/hg18/chromosomes/ as of 13-10-2010
NCBI build 37	FASTA	http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/ as of 13-10-2010
NCBI build 36 Chr 21	FASTA	[Download]
E. coli (MG1655)	FASTA	ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__MG1655 as of 13-10-2010
E. coli (DH10B) Option 1	FASTA	ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__DH10B/ as of 13-10-2010
E. coli (DH10B) Option 2	FASTA	http://solidsoftwaretools.com/gf/project/dh10bfrag/DH10B_WithDup_FinalEdit_validated.fasta.zip as of 13-10-2010
Variant Databases
dbSNP130	TXT	ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/database/b130_archive/ as of 13-10-2010
NA19240¹SNPs	TXT	[Download]
NA19240¹Indels	TXT	[Download]
NA19240&Yoruba²SNPs	TXT	[Download]
NA19240&Yoruba²Indels	TXT	[Download]
NA19240&18507& Yoruba³SNPs	TXT	[Download]
NA19240&18507& Yoruba³Indels	TXT	[Download]
Gene Databases
OMIM genes⁴	BED	[Download]

¹ Consists of those dbSNP 130 variants that were also observed in a capillary sequencing study of NA19240 (Kidd, et al. Nature. 2008 May 1; 453 (7191): 56-64)
² Consists of those dbSNP 130 variants that were also observed in a capillary sequencing study of NA19240 and in at least one other Yoruban individual (of NA18506, NA18507, and NA18508) (Kidd, et al. Nature. 2008 May 1; 453 (7191): 56-64)
³ Consists of those dbSNP 130 variants that were also observed in a capillary sequencing study of NA19240 and NA18507, and at least one other Yoruban individual (of NA18506 and NA18508) (Kidd, et al. Nature. 2008 May 1; 453 (7191): 56-64)
⁴ Also available from http://genome.ucsc.edu/cgi-bin/hgTables?command=start

References

Evaluation of next generation sequencing platforms for population targeted sequencing studies. Harismendy O, et al. Genome Biol. 2009; 10 (3): R32.
Complete Khoisan and Bantu genomes from southern Africa. Schuster SC, et al. Nature. 2010 Feb 18; 463 (7283): 943-947.
Mapping and sequencing of structural variation from eight human genomes. Kidd JM, et al. Nature. 2008 May 1; 453 (7191): 56-64.
Whole exome capture in solution with 3 Gbp of data. Bainbridge MN,et al. Genome Biol. 2010; 11 (6): R62.
Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. McKernan KJ,et al. Genome Res. 2009 Sep; 19 (9): 1527-1541.
Accurate whole human genome sequencing using reversible terminator chemistry. Bentley DR, et al. Nature. 2008 Nov 6; 456 (7218): 53-9.

Tru Resources