Miscellaneous
Miscellaneous
This area holds tutorials and documents put together for elsewhere (that may or may not have ended up somewhere on the site), as well as some older versions of things for archinving purposes.
Archives
USEARCH/VSEARCH amplicon example
This is a command-line example of processing an amplicon dataset followed by initial analyses in R. A more up-to-date version primarily in R is here.
STAMPS
The STAMPS course (Strategies and Techniques for Analyzing Microbial Population Structures) at the Marine Biological Laboratory in Woods Hole, MA, USA.
STAMPS 2018
Introduction to Unix
The basics to working at the command line along with some definitions and philosophy of starting out in bioinformatics can be found here.
Amplicon and Metagenomics overviews
This page presents a broad-level overview of amplicon sequencing and metagenomics as approaches for microbial ecology, discussing some things each is useful and not useful for, and then outlining some general workflows for each.
STAMPS 2019
Introduction to Unix
The basics to working at the command line along with some definitions and philosophy of starting out in bioinformatics can be found here.
DIBSI 2018
DIBSI (Data Intensive Biology Summer Institute) has been a bioinformatics workshop run by Titus Brown for almost a decade. It now happens at UC Davis, USA each year.
Recovering genomes from metagenomes
This tutorial goes through the co-assembly and recovering genomes from a relatively simple system using Anvi’o to demonstrate some of the core concepts.