2014 ismb-extra-slides

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2014 ismb-extra-slides

  1. 1. Extra slides
  2. 2. Do you have a close reference? Mapping or BLASTX => functional inference Assembly Yes! No!
  3. 3. https://etherpad.mozilla.org/ismb2014
  4. 4. Adapter trim & quality filter Diginorm to C=10 Trim high- coverage reads at low-abundance k-mers Diginorm to C=5 Partition graph Split into "groups" Reinflate groups (optional Assemble!!! Map reads to assembly Too big to assemble? Small enough to assemble? Annotate contigs with abundances MG-RAST, etc. The Kalamazoo Metagenomics Pipeline 4
  5. 5. Protocols Web site: khmer- protocols.readthedocs.org/en/latest/metageno mics/

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