Research
Core Genomic Facility
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1. The orientation and organization of CGF 

 

Core Genomic Facility (Abbr: CGF) is a technology-supporting department, which focuses on keep up with the development of genomics and bioinformatics, serving the scientific projects funded by the government, Chinese Academy of Sciences and Beijing Institute of Genomics. CGF is aiming to establish the cutting edge technology and sequencing standard through technical support services and innovation, to establish a “BIG data” system for data collection, storage, management and release, to construct a multi-disciplinary and systematic research platform for functional genome research. CGF is becoming to a comprehensive and systematic technical platform supporting the major scientific research achievements.

 

In 2014 in order to adapt the new development of the institute, new round of reformation is carried out. Now there are 56 technical support personnel in CGF. There are four relatively independent division in CGF as "nucleic acid sequencing division", "bioinformatics analysis division", "information management center" and "instruments sharing platform".

 

 

2. The Technical support progress of CGF

 

CGF is equipped with high-level experimental instruments and high performance computing devices. Now CGF can provide all kinds of sequencing services using the first generation sequencer 3730xl, next generation sequencer Hiseq2000 and FLX 454, the third generation single-molecular sequencer Pacbio RSII. The computation ability has reached 6 million billions Flopy and 6800 TB in storage. The common shared instruments handled by CGF include co-focus microscope, chromatographic instrument et al, can meet the demand of functional genomics research.

 

More than 100 research projects have been carried out by CGF in 2014, including function exploitation project funded by CAS, 973 project, 863 project and other entrusted research projects. We have unique advantages in long fragment genome library construction, minor sample genome library construction, high throughput genome sequencing, single-molecular genome sequencing, de novo genome assembly, transcriptome analysis, epigenome analysis and mutation identification etc. In sequencing field, the second-generation sequencer Hiseq2000 is running smoothly and the third generation single-molecular sequencer has provided technology support in many projects. The Pacbio sequencer has highlighted microorganism genome research and complicated crop genome research.

 

In bioinformatics research field, Bio-informatics Analysis Division has performed a variety of achievements. Analytical pipelines for many kinds of genomic data have been created and many soft and online server have been developed, including GOBOND, MeRIP-PF, wapRNA, CASbreak and so on. Some achievements have obtained software copyright. In "2014 international somatic variation detection global dream challenge", the whole-genome variation detection group ranked the third in "body cell variation detection project challenge " and ranked the fifth in "somatic single base variation project challenge".

 

As to high performance computation and database construction and management, Information management center has accumulated more than 100 TB raw genomic data and developed more than 20 professional databases. The center has provided the data storage and computation analysis service for major project pilot funded by CAS. The project "BIG Genomics Data Center" has been started in 2014, which will gradually achieve the overall management of all kinds of omics data, produced by CAS and has important significance for the data safety all over the country.

 

In 2014 September, the Instruments Sharing Management Platform was established formally, aiming at the optimization in equipment resource and the efficient use of the large-scale instrument and equipment. Since two months, the platform combed and analyzed the technical performance and the running situation of the instruments over 200 thousand yuan and formulated the "The construction and operation scheme of the Instruments Sharing Management Platform (Trial)", "The sharing instruments charging standards (Trial)" and "The using rules of the sharing instruments " etc. A number of technical training has been carried out directing at the professional instruments. The management of the universal sharing instruments has been further standardized.

 

The algorithm for chromosome structure variation detection according to the whole genome sequencing data: CASbreak