TOPIC: Metagenomics
- A working Unix environment (though practice environments are available for lessons below)
- Experience with the command line
- Lesson 1: What is metagenomics?
- Lesson 2: Taxonomic classification using k-mers
- Lesson 3: Taxonomic Classification using MinHash sketches
- Lesson 4: Read mapping and read taxonomic classification
- Lesson 5: Genome and Metagenome Assembly
- Lesson 6: Binning Metagenome-assembled Genomes
- Lesson 7: Bin Evaluation
Date posted: 15 April 2020
Author(s): Dr. Eric Collins
Instructor(s): Dr. Eric Collins
- What kinds of questions can metagenomics be used to answer?
- Is metagenomics right for me?
- Yay! You got data! Now what?
Date posted: 15 April 2020
Author(s): Dr. Alexis Marshall
Instructor(s): Dr. Alexis Marshall
Bash script | Video presentation |
Primary tools/programs used:
- FastQC - FastQC is a quality control tool for high throughput sequence data.
- MultiQC - MultiQC is a quality control summary tool for high throughput sequence data.
Date posted: 18 April 2020
Author(s): Dr. Eric Collins
Instructor(s): Dr. Eric Collins
- The power of k-mers
- Choosing a k-mer classifier
Date posted: 18 April 2020
Author(s): Dr. Eric Collins
Instructor(s): Dr. Eric Collins
Bash script | Video presentation |
Primary tools/programs used:
- bbtools - BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data
- kraken2
- krona
Date posted: 20 April 2020
Author(s): Dr. Ella Sieradzki
Instructor(s): Dr. Ella Sieradzki
Bash script | Video presentation |
Primary tools/programs used:
Date posted: 22 April 2020
Author(s): Dr. Eric Collins
Instructor(s): Dr. Eric Collins
- The Jaccard Index
- How does MinHash work?
- How do Bloom filters work?
- Choosing a MinHash sketcher
Interactive material -- Taxonomic Classification using sourmash and sendsketch, and quality trimming using bbduk
Date posted: 23 April 2020
Author(s): Dr. Eric Collins
Instructor(s): Dr. Eric Collins
Bash Script | Video presentation |
Primary tools/programs used:
- sourmash
- bbtools
Date posted:
Author(s): Dr. Luis Valentin and Dr. Ella Sieradzki
Instructor(s): Dr. Luis Valentin and Dr. Ella Sieradzki
- How does mapping work?
- Choosing a metagenomic read mapper
- The Burrows-Wheeler transform and using bowtie2
Date posted: 27 April 2020
Author(s): Dr. Ella Sieradzki
Instructor(s): Dr. Ella Sieradzki
Bash script | Video presentation |
Primary tools/programs used:
- bbtools
Date posted: 5 May 2020
Author(s): Dr. Ella Sieradzki
Instructor(s): Dr. Ella Sieradzki
Primary tools/programs used:
Date posted: 14 May 2020
Author(s): Dr. Eric Collins and Dr. Ben Tully
Instructor(s): Dr. Eric Collins
- Considerations for approaching assembly and necessary coverage
- Differences between assembler types
Date posted: 14 May 2020
Author(s): Dr. Eric Collins
Instructor(s): Dr. Eric Collins
Bash Script | Video presentation |
Date posted: 6 June 2020
Author(s): Dr. Daan Speth
Instructor(s): Dr. Daan Speth
- Introduction to the principles of metagenome binning
- Highlighted tools: Metabat, BinSanity, DAS Tool
- Discussion of alternative approaches for community deconvolution
Date posted: 6 June 2020
Author(s): Dr. Daan Speth
Instructor(s): Dr. Daan Speth
Primary tools/programs used:
Date posted: 3 August 2020
Author(s): Dr. Daan Speth
Instructor(s): Dr. Daan Speth
- Exploring how to determine the quality of binning outputs
Date posted: 3 August 2020
Author(s): Dr. Daan Speth
Instructor(s): Dr. Daan Speth
Content | Video presentation |
Primary tools/programs used: