2017-cicese-metagenomics
1.0
Site
Environmental Metagenomics Workshop
Welcome!
Start an Amazon Web Services computer:
Intro to Shell Lesson
The Shell
For Future Reference
Finding files
Running command-line BLAST
Short read quality and trimming
Run the MEGAHIT assembler
Evaluating Metagenomic Assemblies
Annotation with Prokka
Comparing datasets using sourmash
A sourmash tutorial
K-mers, k-mer specificity, and comparing samples with k-mer Jaccard distance.
Binning a Metagenomic Assembly
Gene Abundance Estimation with Salmon
Mapping
Slicing and dicing with k-mers
Using Anvi’o to Knit Everything Together
Using and Installing Circos
Workflow and repeatability discussion
Data
Building this site on your own
2017 / September / Environmental Metagenomics
Day 2 - installation instructions
K-mer Spectral Error Trimming
Page
Index