This document outlines the steps in the Kalamazoo Metagenomics Pipeline for analyzing metagenomic sequencing data. The steps include: 1) adapter trimming and quality filtering of reads, 2) normalization of read coverage using Diginorm, 3) partitioning reads into groups and re-inflating groups, 4) assembling reads into contigs, 5) mapping reads back to the assembly, and 6) annotating contigs with abundance information using tools like MG-RAST.

1. Extra slides

2. Do you have a
close reference?
Mapping or
BLASTX =>
functional
inference
Assembly
Yes! No!

3. https://etherpad.mozilla.org/ismb2014

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. Protocols Web site:
khmer-
protocols.readthedocs.org/en/latest/metageno
mics/