Metagenomics Workshop SciLifeLab
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Introduction
Connecting to UPPMAX
Checking required software
Quality Control
Community analysis using 16S reads
Metagenomic Assembly
Annotation
Functional Annotation
Taxonomic annotation
Mapping reads and quantifying genes
Summarize and explore the annotation
Metagenomics Workshop SciLifeLab
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Annotation
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Annotation
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Here you will learn how to annotate your assemblies.
Functional Annotation
PROKKA
Predicting metabolic pathways using MinPath
Taxonomic annotation
DIAMOND
MEGAN
Krona
Mapping reads and quantifying genes
Overview
Mapping reads with bowtie2
Removing duplicates
Counting mapped reads per gene
Normalizing to Transcripts Per Million (TPM)
Summarize and explore the annotation
KRONA interactive plots
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