All tutorials
Below is a list of all the currently available pages. If you have any suggestions of things to add or improve, please feel free to get in touch via twitter or posting an issue 🙂
Unix
- An introduction to Scripting
- An introduction to Conda
- An introduction to Screen
- What the heck is my PATH, and how do I get it to do what I want?
- More automation power (startup files, aliases, and functions)
- Accessing data from NCBI at the command line with EDirect
- Why is this all worth it? (Some everyday examples)
- Help installing tools (this section is now pretty much happily obselete thanks to conda 🙂)
- Other great resources
R
Amplicon analysis
- Demultiplexing example
- A full walkthrough of processing and initial analyses
- An example of dealing with 16S and 18S mixed together
Genomics
- Where to start: quality filtering, error correction, and depth normalization
- de novo genome assembly
- Recovering Metagenome-Assembled Genomes (MAGs) from metagenomes
- An introduction to phylogenomics
Miscellaneous
The miscellaneous area holds tutorials and documents put together for elsewhere as well as some older versions of things solely from this site for archiving purposes. Select ones are linked below, but there are more here.
- An amplicon and metagenomics overview
- Amplicon processing example with USEARCH/VSEARCH (archived version)
- Intro to bash (archived version)
- Six glorious commands (archived version)
- The wonderful world of loops (archived version)