Wang Jian, Yu Jun, Yang Huanming and Liu Siqi created BGI in November 1999  in Beijing, China as a non-governmental independent research institute in order to participate in the Human Genome Project as China's representative. After the project was completed, funding dried up. So BGI moved to Hangzhou in exchange for funding from the Hangzhou Municipal Government.
In 2007 BGI’s headquarters relocated to Shenzhen as "the first citizen-managed, non-profit research institution in China". Yu Jun left BGI at this time purportedly selling his stake to the other 3 founders for a nominal sum.  In 2008, BGI-Shenzhen was officially recognized as a state agency. In 2008, BGI published the first human genome of an Asian individual.
In 2010 BGI Shenzhen was certified as meeting the requirements of ISO9001:2008 standard for the design and provision of high-throughput sequencing services, The same year BGI bought 128 sequencing machines and claimed to be the world's largest genome center.
In 2013 BGI claimed it had relationships with 17 out of the top 20 global pharmaceutical companies. and advertised that it provided commercial science, health, agricultural, and informatics services. That year it bought Complete Genomics of Mountain View, California, a major supplier of DNA sequencing technology, for US$118 million.
The Institute has described itself as partly private and partly public, receiving funds both from private investors and the Chinese government. The laboratory was also the Bioinformatics Center of the Chinese Academy of Sciences.
First to de novo sequence and assemble mammalian and human genomes with short-read sequencing (so-called "next generation sequencing")
Sequenced 40 domesticated and wild silkworms, identifying 354 genes likely important in domestication.
Sequenced the first giant panda genome, equal in size to the human genome, in less than 8 months Sequencing revealed that the giant panda, Ailuropoda melanoleuca, has a frameshift mutation in a gene involved in sensing savory flavors, T1R1. The mutation might be the genetic reason why the panda prefers bamboo over meat. However, the panda also lacks genes expected for bamboo digestion, so its microbiome might play a key role in metabolizing its main source of food.
Key player in the Sino-British Chicken Genome Project
Nature in 2010 ranked BGI Shenzhen as the fourth among the ten top institutions in China with all the others being universities and the Chinese Academy of Sciences. The ranking was based on articles in Nature research journals. There were similar results for other tops journals.
In 2014, BGI was reported to be producing 500 cloned pigs a year to test new medicines.
Current research projects
Yan Huang Project
Started in 2007 and named after two Emperors believed to have founded China’s dominant ethnic group, BGI planned in this project, to sequence at least 100 Chinese individuals to produce a high-resolution map of Chinese genetic polymorphisms. The first genome data was published in October 2007. An anonymous Chinese billionaire donated $10 million RMB (about US$1.4 million) to the project and his genome was sequenced at the beginning of the project.
Diabetes-associated Genes and Variations Study (LUCAMP) Cancer Genome Project
Nine Danish universities and institutes will collaborate with BGI in this targeted resequencing project.
BGI explores associated genome and gene variation in complexes diseases in large-scale studies primarily using two methods: PCR-based resequencing of candidate genes and exon-capture-based whole exome resequencing.
Cognitive Research Lab
The Cognitive Research Lab at BGI is working with Stephen Hsu on a project to discover the genetic basis of human intelligence.
Animals and plants
1,000 Plant and Animal Reference Project
BGI is leading an international collaboration to sequence 1,000 plants and animals of economic and scientific import within two years. It has pledged an initial US$100 million to start the program.
BGI has already sequenced genomes of 20 species of animals and 9 species of plants—sometimes for multiple individuals, such as 40 silkworms 19713493, and has an equal number underway as of March 2010[update].
Three Extreme-Environment Animal Genomes Project
A jointly funded project announced March 19, 2010, BGI will collaborate with Sidney K. Pierce of University of South Florida and Charles Delwiche of the University of Maryland at College Park to sequence the genomes of the sea slug, Elysia chlorotica, and its algal food Vaucheria litorea. The sea slug uses genes from the algae to synthesize chlorophyll, the first interspecies of gene transfer discovered. Sequencing their genomes could elucidate the mechanism of that transfer.
De novo sequencing requires aligning billions of short strings of DNA sequence into a full genome, itself three billion base pairs long for humans.
BGI’s computational biologists developed the first successful algorithm, based on graph theory, for aligning billions of 25 to 75-base pair strings produced by next-generation sequencers, specifically Illumina’s Genome Analyzer, during de novo sequencing. The algorithm, called SOAPdenovo, can assemble a genome in two days and has been used to sequence an array of plant and animal genomes.
BGI’s 500-node supercomputer processes 10 terabytes of raw sequencing data every 24 hours from its current 30 or so Genome Analyzers from Illumina. The annual budget for the computer center is US$9 million.
SOAPdenovo is part of "Short Oligonucleotide Analysis Package" (SOAP), a suite of tools developed by BGI for de novo assembly of human-sized genomes, alignment, SNP detection, resequencing, indel finding, and structural variation analysis. Built for the Illumina sequencers' short reads, SOAPdenovo has been used to assemble multiple human genomes (identifying an eight kilobase insertion not detected by mapping to the human reference genome) and animals, like the giant panda.
^ abRasmussen, M.; Li, Y.; Lindgreen, S.; Pedersen, J. S.; Albrechtsen, A.; Moltke, I.; Metspalu, M.; Metspalu, E.; Kivisild, T.; Gupta, R.; Bertalan, M.; Nielsen, K.; Gilbert, M. T. P.; Wang, Y.; Raghavan, M.; Campos, P. F.; Kamp, H. M.; Wilson, A. S.; Gledhill, A.; Tridico, S.; Bunce, M.; Lorenzen, E. D.; Binladen, J.; Guo, X.; Zhao, J.; Zhang, X.; Zhang, H.; Li, Z.; Chen, M.; Orlando, L. (2010). "Ancient human genome sequence of an extinct Palaeo-Eskimo". Nature463 (7282): 757–762. doi:10.1038/nature08835. PMC3951495. PMID20148029.edit
^"BGI". Archived from the original on 17 February 2010. Retrieved 29 March 2010.
^Cho, Y. S.; Hu, L.; Hou, H.; Lee, H.; Xu, J.; Kwon, S.; Oh, S.; Kim, H. M.; Jho, S.; Kim, S.; Shin, Y. A.; Kim, B. C.; Kim, H.; Kim, C. U.; Luo, S. J.; Johnson, W. E.; Koepfli, K. P.; Schmidt-Küntzel, A.; Turner, J. A.; Marker, L.; Harper, C.; Miller, S. M.; Jacobs, W.; Bertola, L. D.; Kim, T. H.; Lee, S.; Zhou, Q.; Jung, H. J.; Xu, X. et al. (2013). "The tiger genome and comparative analysis with lion and snow leopard genomes". Nature Communications4. doi:10.1038/ncomms3433.edit