Metagenomics



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tarix14.01.2017
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Metagenomics











  • How do you generate consistent and accurate annotations for metagenomes?





FIG developed the notion of Subsystem – a generalization of “pathway” as a collection of functional roles jointly involved in a biological process or complex

  • FIG developed the notion of Subsystem – a generalization of “pathway” as a collection of functional roles jointly involved in a biological process or complex

  • Extended subsystems into FIGfams – protein families that perform the same functions.



Automated user originated processing

  • Automated user originated processing

  • Takes 1-7 hours depending on size and complexity of the genome

  • ~2,000 external submissions, including hundreds of genomes not yet publicly released.

  • Reannotation of >500 genomes complete

  • 1,000 users, 200 organizations, 25 countries.



















~19 hours of compute per input megabyte

  • ~19 hours of compute per input megabyte



  • 986 metagenomes

  • 79,417,238 sequences

  • 17,306,834,870 bp (17 Gbp)

  • Average: ~15-20 M bp per genome

  • Compute time (on a single CPU):

  • 328,814 hours = 13,700 days = 38 years









Free workshops on NMPDR, RAST, mg-RAST, SEED

  • Free workshops on NMPDR, RAST, mg-RAST, SEED

  • Contact Leslie McNeil

  • lkmcneil@ncsa.uiuc.edu

  • or visit

  • http://www.nmpdr.org/












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