Week 11: Poster Presentations (SW) Cloud Computing and Jupyter Notebooks
The purpose and objective:
The objective of lab is to learn Qiime2 and Terminal and install the Qiime2.
Date: 04/04/19
Procedures:
Install Qiime2
- Download the Miniconda with 64-bit (.pkg installer) and install it
- Type “conda update conda”
- Then, type “conda install wget”
- Type “y” after the formula
- Copy two lines to the terminal
- Then return, and loading it for few minutes
Command
- Use “research” to open terminal
- Type “say something you want to talk”, then it will talk what you type in the terminal
- Type “cd~/Documents” and press return to go to the home folder
- Type ls then you will see the lists of document
- Type mkdir “TerminalTest” to create a new folder
Words about Qiime2 from QTM
- Qiime
The full name of Qiime is Quantitative Insights Into Microbial Ecology. Qiime is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
- Demultiplex
Demultiplex is a method by which multiple analog message signals or digital data streams are combined into one signal over a shared medium.
- Denoise
Denoise is the process of removing and/or correct noisy from a signal.
- Feature Table
The feature table is a figure that consists of a header line, which contains the column titles for the table, and the individual feature entries.
- Alignment
In QIIME, plugin provides support for generating and manipulating sequence.
- Phylogeny
Phylogenetics is the study of evolutionary relationships among groups of organisms, which are discovered through molecular sequencing data and morphological data matrices.
- Diversity Analysis
Diversity Analysis is combined several QIIME to form a basic workflow beginning with a BIOM table, mapping file, and optional phylogenetic tree.
Conclusion and The Future Goal:
In today’s lab, I learn the Qiime2 that is a very powerful microbiome analysis package. Also, it could help us to analysis different classification and the relative abundance of species of our soil sample. In the future, I hope to learn more about soil ciliates diversity through the Qiime2.