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Author: AstrobioMike

amplicon/dada2_workflow_ex.md

@@ -27,7 +27,7 @@ Keep in mind here that just as was the case with the [usearch/vsearch example wo
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 # Tools used here
-So here we'll be using [DADA2](https://benjjneb.github.io/dada2/index.html){:target="_blank"} as our main processing tool. Additionally we'll be using [Brian Bushnell's](https://twitter.com/BBToolsBio){:target="_blank"} very handy [bbtools](https://jgi.doe.gov/data-and-tools/bbtools/){:target="_blank"}, specifically [bbduk](https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/){:target="_blank"}, to remove our primers and perform quality trimming. DADA2 is available as an [R](https://www.r-project.org/){:target="_blank"} package, with installation instructions provided by the developers [here](https://benjjneb.github.io/dada2/dada-installation.html){:target="_blank"}. If your experience is like mine, it shouldn't give you any trouble if installing on your computer, but you may run into some issues when trying to install on a server where you don't have authorization to do whatever you'd like (a huge thanks to [@phantomBugs](https://twitter.com/phantomBugs){:target="_blank"} for all his help when I was bugging him about that 🙂). If you'd like to use [bbtools](https://jgi.doe.gov/data-and-tools/bbtools/){:target="_blank"}, you can find installation instructions for it from the developers [here](https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/installation-guide/) and another example installation [here](/bash/installing_tools#bbtools){:target="_blank"}.
+So here we'll be using [DADA2](https://benjjneb.github.io/dada2/index.html){:target="_blank"} as our main processing tool. Additionally we'll be using [Brian Bushnell's](https://twitter.com/BBToolsBio){:target="_blank"} very handy [bbtools](https://jgi.doe.gov/data-and-tools/bbtools/){:target="_blank"}, specifically [bbduk](https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/){:target="_blank"}, to remove our primers. DADA2 is available as an [R](https://www.r-project.org/){:target="_blank"} package, with installation instructions provided by the developers [here](https://benjjneb.github.io/dada2/dada-installation.html){:target="_blank"}. If your experience is like mine, it shouldn't give you any trouble if installing on your computer, but you may run into some issues when trying to install on a server where you don't have authorization to do whatever you'd like (a huge thanks to [@phantomBugs](https://twitter.com/phantomBugs){:target="_blank"} for all his help when I was bugging him about that 🙂). If you'd like to use [bbtools](https://jgi.doe.gov/data-and-tools/bbtools/){:target="_blank"}, you can find installation instructions for it from the developers [here](https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/installation-guide/) and another example installation [here](/bash/installing_tools#bbtools){:target="_blank"}.
 
 And since dada2 is an R package, you also of course need to have a working installation of R on your computer. If you'd like more info on this, check out the [R basics](/R/basics){:target="_blank"} section before moving forward. 
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