This readme.txt file was generated on 20160421 by Georgia Huang


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GENERAL INFORMATION
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1. Title of Dataset 
Regions of High Confidence in Chinese Hamster and CHO-K1 Genome Assemblies

2. Author Information

  Principal Investigator Contact Information
           Name: Vishwanathan, Nandita
           Institution: Takeda Pharmaceutical Company Limited
           Address: Osaka, Kanagawa, Japan


  Associate or Co-investigator Contact Information
         A.Name: Bandyopadhyay, Arpan
           Institution: University of Minnesota
           Email: bandy016@umn.edu


         B.Name: Fu, Hsu-Yuan
           Institution: University of Minnesota
           Email: fuh@umn.edu


         C.Name: Sharma, Mohit
           Institution: University of Minnesota
           Email: sharm163@umn.edu


         D.Name: Johnson, Kathryn



         E.Name: Mudge, Joann
           Institution: National Center for Genome Resources
           Address: Santa Fe, New Mexico 87505 USA


         F.Name: Ramaraj, Thiruvarangan
           Institution: National Center for Genome Resources
           Address: Santa Fe, New Mexico 87505 USA


         G.Name: Onsongo, Getiria
           Institution: University of Minnesota
           Email: onsongo@cs.umn.edu


         H.Name: Silverstein, Kevin A. T.
           Institution: Minnesota Supercomputing Institute
           Email: kats@umn.edu


         I.Name: Jacob, Nitya M.


         J.Name: Le, Huong
           Institution: University of Minnesota
           Email: lexxx469@umn.edu


         K.Name: Karypis, George
           Institution: University of Minnesota
           Email: karypis@cs.umn.edu


         L.Name: Hu, Wei-Shou
           Institution: University of Minnesota
           Email: wshu@umn.edu


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SHARING/ACCESS INFORMATION
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1. Licenses/restrictions placed on the data: 
Embargoed until 2018-04-05. 


2. Links to publications that cite or use the data:
To be updated


3. Was data derived from another source?
           If yes, list source(s): 
                   A. AMDS00000000.1 Chinese hamster genome assembly from NCBI
                   B. UMN1.0 in-house genome assembly
                   C. AFTD00000000.1 CHO-K1 genome assembly of CHO-K1 from NCBI


4. Recommended citation for the data:
Vishwanathan, Nandita; Bandyopadhyay, Arpan; Fu, Hsu-Yuan; Sharma, Mohit; Johnson, Kathryn; Mudge, Joann; Ramaraj, Thiruvarangan; Onsongo, Getiria; Silverstein, Kevin A. T.; Jacob, Nitya M.; Le, Huong; Karypis, George; Hu, Wei-Shou. (2016). Regions of High Confidence in Chinese Hamster and CHO-K1 Genome Assemblies. Retrieved from the University of Minnesota Digital Conservancy, http://dx.doi.org/10.13020/D6Z304.



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DATA & FILE OVERVIEW
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1. File List
   A. Filename: HCR_AMDS00000000.bed       
      Short description: Bed file containing the scaffold ID, start and end positions of the 'high confidence regions' in AMDS00000000.1 draft assembly of Chinese hamster genome with in-house UMN1.0      


        
   B. Filename: HCR_AFTD00000000.bed   
      Short description: Bed file containing the scaffold ID, start and end positions of the 'high confidence regions' in AFTD00000000.1 draft assembly of CHO-K1 genome with AMDS00000000.1 draft assembly of Chinese hamster genome.     




2. Relationship between files:     
Both bed files used AMDS00000000.1 draft assembly of Chinese hamster genome as part of the input.



3. Are there multiple versions of the dataset? no



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METHODOLOGICAL INFORMATION
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1. Description of methods used for collection/generation of data: 
Three genome assemblies were used for comparison. In addition to the in-house genome assembly UMN1.0, two public genome assemblies AMDS00000000.1 and AFTD00000000.1 were obtained from the NCBI Nucleotide Database.  


2. Methods for processing the data:
The genomes were compared by whole genome alignments using NUCmer (Kurtz et al. 2004). The regions of consensus between the two drafts were filtered using with a stringent criterion of contiguous segments larger than 1 Kbp with sequence identity greater than 97 % matching to unique reference and query sequence. This information was then converted into the bed files.

3. Instrument- or software-specific information needed to interpret the data:
The bed files can be used in a genome browser such as Integrative Genomics Viewer (IGV).