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Do you have a
close reference?
Mapping or
BLASTX =>
functional
inference
Assembly
Yes! No!
https://etherpad.mozilla.org/ismb2014
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
Protocols Web site:
khmer-
protocols.readthedocs.org/en/latest/metageno
mics/

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