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Protocols

Platinum Genomes specifications

Information


Unique identifier OMICS_12060
Name Platinum Genomes
Restrictions to use None
Community driven No
Data access File download
User data submission Not allowed
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Publication for Platinum Genomes

Platinum Genomes citations

 (15)
library_books

EAGLE: Explicit Alternative Genome Likelihood Evaluator

2018
BMC Med Genomics
PMCID: 5918433
PMID: 29697369
DOI: 10.1186/s12920-018-0342-1

[…] NA12878 (cell line of an individual from a CEPH pedigree), using an exome sequencing dataset (Garvan HG001) from Genome-In-A-Bottle (GIAB) [] and a 200× whole genome sequencing dataset from Illumina Platinum Genomes (IPG). The benchmark from IPG consists of a high confidence callset for the GRCh38 human reference genome constructed using FreeBayes, Platypus, and GATK variant callers. The benchmar […]

library_books

Nanopore sequencing and assembly of a human genome with ultra long reads

2018
Nat Biotechnol
PMCID: 5889714
PMID: 29431738
DOI: 10.1038/nbt.4060

[…] er ones ().To quantify deviations from the expected 50:50 allele ratio at heterozygous sites, 25,541 homozygous and 46,098 heterozygous SNP positions on chromosome 20 were extracted from the Illumina Platinum Genomes project VCF for GM12878, requiring a minimum distance of 10 bp between SNP positions. Scrappie base calls at these positions were extracted using samtools mpileup. Deviation from the […]

library_books

Scalability and Validation of Big Data Bioinformatics Software

2017
Comput Struct Biotechnol J
PMCID: 5537105
PMID: 28794828
DOI: 10.1016/j.csbj.2017.07.002

[…] nce standards, methods and data for whole human genome sequencing. Reference data sets can also be obtained from the manufacturer of the particular sequencing machine – e.g., Illumina's The BaseSpace Platinum Genomes Project and the Variant Calling Assessment Tool (VCAT) . While this approach is a good starting point, it only verifies a very limited number of input/output combinations. All humans […]

library_books

Intersect then combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers

2017
Genome Med
PMCID: 5394620
PMID: 28420412
DOI: 10.1186/s13073-017-0425-1

[…] We sequenced two cell lines from the HapMap/1000 Genomes Project, NA12878 (Platinum Genomes) and NA11840 to mimic a tumour-normal pair allowing identification of ‘somatic’ SNVs and indels. The NA12878 sample was also mixed with an increasing amount of NA11840 (up to 99.8% by […]

call_split

Genetic and regulatory mechanism of susceptibility to high hyperdiploid acute lymphoblastic leukaemia at 10p21.2

2017
Nat Commun
PMCID: 5337971
PMID: 28256501
DOI: 10.1038/ncomms14616
call_split See protocol

[…] ata for proteins binding to either loci was downloaded from Encode (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/) and whole genome fastq data for the GM12878 was downloaded from Illumina Platinum Genomes project (AC:ERR194147). Fastq data were aligned to the human reference genome (human_g1k_v37), edited to mask common SNPs in build 141, using Stampy v1.0.28 sequence alignment tool. A […]

library_books

CRISPR–Cas9 targeted fragmentation and selective sequencing enable massively parallel microsatellite analysis

2017
Nat Commun
PMCID: 5309709
PMID: 28169275
DOI: 10.1038/ncomms14291

[…] GS of the HapMap sample NA12878, as a ground truth set. This sample was subject to Illumina-sequencing at an average coverage of 200 × on a HiSeq 2000 system, using an amplification-free library. The platinum genomes vcf file was downloaded from Illumina and filtered with vcftools using the following filters: --thin 6 --remove-filtered-all --remove-indels --recode --recode-INFO-all, and with --bed […]

Citations

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Platinum Genomes institution(s)
Illumina Inc., San Diego, CA, USA; Illumina Ltd., Chesterford Research Park, Little Chesterford, UK; Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, UK; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK

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