2017-dibsi-metagenomics
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2017 DIBSI Metagenomics Workshop at UC Davis
Welcome!
Booting a Jetstream Computer Instance for your use!
Intro to Shell Lesson
The Shell
For Future Reference
Finding files
Running command-line BLAST
Short read quality and trimming
Run the MEGAHIT assembler
Annotation with Prokka
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 / July / Environmental Metagenomics
Day 2 - installation instructions
K-mer Spectral Error Trimming
Page
Table of Contents
2017 DIBSI Me... »
Source
Table of Contents
ΒΆ
Tutorials:
2017 DIBSI Metagenomics Workshop at UC Davis
Monday, Day 1:
Tuesday, Day 2:
Wednesday, Day 3:
Thursday, Day 4:
Friday, Optional Day 5: TBD (plotting, visualization, jupyter notebooks...)
Undone
Technical information
Welcome!
1. Learning goals
2. Safe space and code of conduct
3. Instructor introductions
4. Jetstream and cloud computing - why?!
5. Sticky notes and how they work... + Minute Cards
Booting a Jetstream Computer Instance for your use!
Request to log in to the Jetstream Portal
Use “XSEDE”
Fill in the username and password and click “Sign in”
Select Projects and “Create New Project”
Name the project for yourself, click “create”
Select the newly created project
Within the project, select “new”
Find the “Ubuntu 16.04” image, click on it
Name it something simple and select ‘m1.medium’
Wait for it to become active
Click on your new instance to get more information!
Miscellany
Suspend your instance
Shutting down your instance
Deleting your 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
Annotation with Prokka
Installing Prokka
Running Prokka
Questions?
Install Kraken
Install Kraken Mini DB
Running Kraken
Install Prodigal
Running Prodigal
References
A sourmash tutorial
Objectives
At the beginning
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
Make and search a database quickly.
Compare many signatures and build a tree.
What’s in my metagenome?
Final thoughts on sourmash
Binning a Metagenomic Assembly
Installing binners
Get a rough count of the total number of reads mapping
Binning 1 - MaxBin
Binning 2 - MetaBAT
Visualizing the bins
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
Identifing 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 / July / 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)
--
fork @ github
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