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
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Table of Contents
Environmental... »
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Table of Contents
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Tutorials:
Environmental Metagenomics Workshop
26 - 29 September 2017 at CICESE
Welcome!
1. Learning goals
2. Safe space and code of conduct
3. Instructor introductions
4. Amazon Web Service and cloud computing - why?!
5. Sticky notes and how they work
Start an Amazon Web Services computer:
0. Select “EC2 - virtual servers in the cloud”
1. Switch to zone US West (N California)
2. Click on “Launch instance.”
3. Select “Community AMIs.”
4. Search for ami-05384865 (ubuntu-wily-15.10-amd64-server)
5. Click on “Select.”
6. Choose m4.xlarge.
7. Click “Review and Launch.”
8. Click “Launch.”
9. Select “Create a new key pair.”
10. Enter name ‘amazon-key’.
11. Click “Download key pair.”
12. Click “Launch instance.”
13. Select View instances (lower right)
14. Bask in the glory of your running instance
Intro to Shell Lesson
The Shell
Learning Objectives
What is the shell?
How to access the shell
Mac
Windows
Starting with the shell
Arguments
The Unix directory file structure (a.k.a. where am I?)
Moving around the file system
Examining the contents of other directories
Saving time with shortcuts, wild cards, and tab completion
Command History
Examining Files
Searching files
Redirection
Creating, moving, copying, and removing
Running programs
For Future Reference
Finding files
Where can I learn more about the shell?
Bonus:
Running command-line BLAST
Updating the software on the machine
Running BLAST
Short read quality and trimming
Installing software for the workshop
Running Jupyter Notebook
Data source
1. Copying in some data to work with.
1. Copying data into a working location
2. FastQC
3. Trimmomatic
4. FastQC again
5. MultiQC
Run the MEGAHIT assembler
While the assembly runs...
After the assembly is finished
Evaluating Metagenomic Assemblies
Annotation with Prokka
Installing Prokka
Running Prokka
Questions?
References
Comparing datasets using sourmash
A sourmash tutorial
Objectives
K-mers, k-mer specificity, and comparing samples with k-mer Jaccard distance.
K-mers!
K-mers and assembly graphs
Why k-mers, though? Why not just work with the full read sequences?
Long k-mers are species specific
Using k-mers to compare samples against each other
Installing sourmash
Generate a signature for Illumina reads
Compare reads to assemblies
Compare signatures.
Binning a Metagenomic Assembly
Installing binners
Binning 1 - MaxBin
Binning 2 - MetaBAT
Visualizing the bins
Optional
Gene Abundance Estimation with Salmon
Installing Salmon
Running Salmon
Working with count data
Plotting the results
References
Mapping
Downloading data
Mapping the reads
Converting to BAM to visualize
Visualizing the read mapping
Slicing and dicing with k-mers
Assemble the slice
Using Anvi’o to Knit Everything Together
Installing anvi’o (and a few other programs)
Getting it into Anvi’o format
Mapping data
Generating contigs database
Identifying and refining genome bins
Using and Installing Circos
Installing Circos
Visualizing Gene Coverage and Orientation
References
Workflow and repeatability discussion
Data
Building this site on your own
2017 / September / Environmental Metagenomics
Day 2 - installation instructions
Running Jupyter Notebook
K-mer Spectral Error Trimming
Why (or why not) do k-mer trimming?
LICENSE:
This documentation and all textual/graphic site content is released under
Creative Commons - 0 (CC0)
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fork @ github
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