A lot of metagenomics analysis is done using command-line tools for three reasons:
1) You will often be working with a large number of files, and working through the command line rather than through a graphical user interface (GUI) allows you to automate repetitive tasks.
2) You will often need more computing power than is available on your personal computer, and connecting to and interacting with remote computers requires a command-line interface.
3) You will often need to customize your analyses, and command-line tools often enable more customization than the corresponding GUI tools (if a GUI tool even exists).
In a previous lesson, you learned how to use the bash shell to interact with your computer through a command-line interface. In this lesson, you will be applying this new knowledge to
carry out a common metagenomics workflow - identifying Operational Taxonomic Unities (OTUs)
among samples taken from two metagenomes within a location. We will be starting with a set
of sequenced reads (.fastq files), perform some quality control steps, assemble those
reads into contigs and finishes by identifying and visualizing the OTUs among these samples.
As you progress through this lesson, keep in mind that even if you aren’t going to be doing this same workflow in your research, you will be learning some very important lessons about using command-line bioinformatics tools. What you are going to learn here will enable you to use a variety of bioinformatics tools with confidence and greatly enhance your research efficiency and productivity.
Prerequisites
This lesson assumes a working understanding of the bash shell. If you haven’t already completed the Introduction to the Command Line for Metagenomics lesson, and you aren’t familiar with the bash shell; please review those materials before starting this lesson.
This lesson also assumes some familiarity with biological concepts, including the structure of DNA, nucleotide abbreviations, and the concepts microbiome and taxonomy.
This lesson uses data hosted on an Amazon Machine Instance (AMI). Workshop participants will be given information on how to log in to the AMI during the workshop. Learners using these materials for the self-directed study will need to set up their own AMI. Information on setting up an AMI and accessing the required data is provided on the Metagenomics Workshop setup page.
Things You Need To Know
- Stay calm, and don’t panic.
- Everything is going to be fine.
- We are learning together.
This is the fourth lesson of the Metagenomics Workshop comprised of four lessons in total.
Lesson Reference
Episodes 2. Assessing Read Quality, and 3. Trimming and Filtering are adapted from the corresponding episodes in the Data Wrangling and Processing for Genomics lesson.