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Optimized Iterative De Bruijn Graph Assembly

eagle-i ID

http://eagle-i.itmat.upenn.edu/i/0000013a-b805-4d4b-d69a-d90d80000000

Resource Type

  1. Algorithmic software suite

Properties

  1. Related grant number
    Human Microbiome Roadmap Demonstration Project UH2DK083981
  2. Resource Description
    OptItDBA is "a BASH script that will iteratively assemble a set of paired-end metagenomic reads." In each iteration of the optimized iterative de Bruijn graph assembly pipeline, "OptItDBA: (1) selects the optimal kmer, (2) generates a de Bruijn graph for the optimal kmer length, (3) removes the reads that map to the most highly abundant contigs from the dataset or reads that map to circular contigs, and (4) starts another iteration using all of the reads that do not map to those contigs. The loop ends when there are no highly abundant contigs meeting the criteria outlined below. At that point, all of the remaining reads will be assembled and mapped using the optimal values from the final iteration."
  3. Additional Name
    OptItDBA
  4. Used by
    Bushman Laboratory
  5. Operating System
    Unix
  6. Data Input
    Paired-end metagenomic sequence reads
  7. Data Output
    Complete and partial genome sequences (contigs)
  8. Software purpose
    Sequence alignment objective
  9. Related Publication or Documentation
    Conservation of Gene Cassettes Among Diverse Viruses of the Human Gut
  10. Website(s)
    http://microb230.med.upenn.edu/tutorials/optitdba#OptItDBA
  11. Related Technique
    Genome assembly
  12. Related Technique
    Metagenomics analysis
  13. Developed by
    Bushman, Frederic D., PhD
  14. Developed by
    Minot, Samuel
  15. Algorithm used
    de Bruijn graph-based method
 
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The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016