3 ways to run commands in mothur: interactively, with a batch file, and at the command line (CC046)
Channel: Riffomonas Project
Date: 2020-11-09

mothur is a popular tool for analyzing 16S rRNA gene sequences. In this episode, Pat Schloss shows three ways to run commands from mothur and how to incorporate mothur commands into reproducible bash scripts. This episode is part of a larger arc of episodes investigating the sensitivity and specificity of amplicon sequence variants (ASVs), also known as exact sequence variants (ESVs). ASVs are growing in popularity for analyzing microbial communities using 16S rRNA gene sequences. Pat demonstrates these concepts by live coding at the command line interface using RStudio, GitHub Flow, and make.

0:00 Introduction
3:06 Splitting out ESV code
14:05 Interactive mode in mothur
16:10 Batch file mode in mothur
17:28 Command line mode in mothur
21:04 Using the current options in mothur
23:13 Generating ASVs using mothur
36:48 Conclusion

The accompanying blog post contains the exercises and solutions can be found at http://www.riffomonas.org/code_club/2020-11-09-mothur