2017-lapaz-assembly
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2017-lapaz-assembly
A day of assembly in La Paz, MX!
Running BLAST from the command line to identify environmental sequences
Introduction
Workflows and computing!
Run the MEGAHIT assembler
How assembly works
A sourmash tutorial
Intro to QIIME for amplicon analysis
Bonus Material
Resources and help
Working with the OTU table in QIIME
Where to find QIIME resources and help
3.1 Make resemblance matrices to analyze comparative (beta) diversity
3.2 Using QIIME for visualization: Ordination
YOU DID IT! HOLIDAY! CELEBRATE!
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Welcome to the La Paz workshop site!
Indices and tables
2017-lapaz-assembly »
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Welcome to the La Paz workshop site!
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2017-lapaz-assembly
Configuration information
A day of assembly in La Paz, MX!
Schedule
Running BLAST from the command line to identify environmental sequences
Overarching Goal
Learning Objectives
Introduction
Motivation: Why would I want to run BLAST locally?
Step 1: Installing BLAST
Step 2: Download the databases
Step 3: Run BLAST
Exercise
Different BLAST options
Workflows and computing!
Workflows, and responsible conduct of computational research
Reading material
Run the MEGAHIT assembler
While the assembly runs...
After the assembly is finished
How assembly works
A sourmash tutorial
Installing sourmash
Fingerprint reads
Compare reads to assemblies
Make and search a database quickly.
Compare many signatures and build a tree.
What’s in my metagenome?
Intro to QIIME for amplicon analysis
Overarching Goal
Learning Objectives
1.1 Getting started
1.2 Assembling Illumina paired-end sequences
1.3 Understanding the QIIME mapping file
1.4 Getting assembled reads into the one big data file, and extracting summary information
1.5 Picking Operational Taxonomic Units, OTUs.
Bonus Material
1.5.3 Exploring results from OTU picking workflow
Resources and help
QIIME
Biom format
Working with the OTU table in QIIME
2.1 Summarize an OTU table
2.3 Calculating within-sample (alpha) diversity
2.4 Visualizing within-sample diversity
Where to find QIIME resources and help
3.1 Make resemblance matrices to analyze comparative (beta) diversity
3.2 Using QIIME for visualization: Ordination
3.3 Other visualizations in QIIME
3.4 “Collapse” the biom table across DNA extraction replicates
YOU DID IT! HOLIDAY! CELEBRATE!
Help and other Resources
Indices and tables
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Index
Module Index
Search Page