Purpose: The purpose of this lab to be able to learn how to use certain commands from the QiimeWiki and apply them on our apple computer terminal (MacOS). We did this so we could run Qiime once we were able to access atmosphere of Cyverse.

Procedure:

1. Open the terminal of the Apple Computer
2. Go on google and download the “64 bit miniconda .pkg” from https://docs.conda.io/en/latest/miniconda.html
3. Once its down downloading, close the terminal and reopen
4. Type “conda update conda” on the terminal and wait a couple of seconds for it to be running
5. Type “conda install wget” and wait a couple of seconds for it to be installed
6. Type “wget https://data.qiime2.org/distro/core/qiime2-2019.1-py36-osx-conda.yml conda env create -n qiime2-2019.1 –file qiime2-2019.1-py36-osx-conda.yml”. This should take a couple of minutes to run
7. Type “source activate qiime2-2019.1” to activate the qiime program
8. If no error has occurred in downloading this program, then the program has been successfully installed into the terminal
9. Practice using other commands available for the program and terminal.

Vocabulary Learned:

1.      Qiime: A powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.

2.      Demultiplex: performs quality control of sequences through QIIME

3.      Denoise: removes unwanted sequences that don’t match your sequences

4.      Feature Table: defines the logical tree structure of features and contains the columns shown in the table

5.      Alignment: removes certain noise that can affect the sequences. Makes the sequences match.

6.      Phylogeny: the study of evolution, diversity, and the way different organisms and species are related to each other.

7.      Diversity Analysis: Alpha and beta diversity analysis. Applies related statistical test, and generates interactive visualizations.

Commands Learned:

1. used the Say [command] (computer read out what we typed)
2. mkdir letsgetcilli (creates the fil “Letsgetcilli”)
3. ls (allows us to see the list of files in our computer)
4. used the “conda update conda” command (Update the miniconda application)

Conclusion/Future Steps: After completing this lab, we were successfully able to download the Qiime program into our terminal for later use once everybody has access to Cyverse. Running the Qiime program allowed us to access new commands and practiced a couple of those commands and a couple of others that the terminal already knew. We still need to continue to learn how to use Qiime and its commands properly so once we start doing cloud computing , we will know what we are doing when running data. When everyone has access to Cyverse, we will able to start using atmosphere to start cloud computing using the samples from the Chelex and eDNA extraction method.