---
# System prepended metadata

title: Sequencing of phage genomes
tags: [ebook]

---

---
tags: ebook
---


# Sequencing of phage genomes 


 
## Chapter type: Course-based research

* Lab Management and Prep (ordering, accounts, reagents, equipment)
    * Flavors: Quick start
* Molecular biology (a specific lab protocol, e.g., DNA extraction, library prep)
    * Flavors: Tutorial, Lesson
* Bioinformatics (data management and analysis)
    * Flavors: Quick start, tutorials, lessons
 
## Flavor:
* Quick start: usually a page, focuses on achieving one goal, does not cover background information
* Tutorial: walks through a demonstration of a technique with the goal of helping the learner understand
* Lesson: Provides ample background information, has questions and answers to test learner understanding
 
## Media:
 
*  Videos, animations, figures
 

 
LAB MANAGEMENT TEMPLATE (QUICK START)
 
TITLE: Laboratory Materials
## SUMMARY:
This tutorial can be used to isolate phages from soil and sequence their genomes using Nanopore sequencing technology.

 
## MATERIALS:


### For phage isolation from soil:
[SEA-PHAGES Ordering Guide](https://seaphagesphagediscoveryguide.helpdocsonline.com/9-1-protocol)

### For Nanopore sequencing:

#### DNA Extraction Supplies
* 1 ml phage lysate (titer ≥ 5 x 10<sup>9</sup> pfu/ml)
* Nuclease mix
* EDTA (0.5 M) (optional)
* Proteinase K (20 mg/ml) and SDS (10 %) (optional)
* 2 ml DNA clean-up resin (Promega Wizard DNA Clean-Up Kit)
* 2 DNA clean-up columns (Promega Wizard DNA Clean-Up Kit)
* 3 ml syringes
* 6 ml 80 % isopropanol, freshly prepared
* ddH2O pre-warmed (95 &deg;C)

#### Library preparation and sequencing:

* Ligation sequencing gDNA - Native Barcoding Kit 24 V14 (SQK-NBD114.24)
* MinION or MinIONmk1C


 
## PROTOCOL

### SEA-PHAGES protocol for phage isolation
* [Collecting Environmental Samples](https://seaphagesphagediscoveryguide.helpdocsonline.com/5-1-protocol) 
* [Direct Isolation](https://seaphagesphagediscoveryguide.helpdocsonline.com/5-2-protocol)
* [Plaque Assay](https://seaphagesphagediscoveryguide.helpdocsonline.com/5-3-protocol)
* [Picking a Plaque](https://seaphagesphagediscoveryguide.helpdocsonline.com/5-4-protocol)
* [Enriched Isolation](https://seaphagesphagediscoveryguide.helpdocsonline.com/5-5-protocol)
* [Spot Test](https://seaphagesphagediscoveryguide.helpdocsonline.com/5-6-protocol)

### SEA-PHAGES protocol for phage purification
[Phage purification](https://seaphagesphagediscoveryguide.helpdocsonline.com/6-0-toc)

### SEA-PHAGES protocol for DNA extraction
[DNA Extraction](https://seaphagesphagediscoveryguide.helpdocsonline.com/9-1-protocol) 

### Library Preparation
[Ligation sequencing gDNA - Native Barcoding Kit 24 V14 (SQK-NBD114.24)](https://seaphagesphagediscoveryguide.helpdocsonline.com/9-1-protocol)


Optional elements
Media (Figures, animations, videos)
Admonitions (Warnings, tips, etc.)
 
 
 
MOLECULAR BIOLOGY (TUTORIAL)
 
TITLE: Phage Isolation
 
SUMMARY: Students will collect soil samples to isolate phages
TIME: Estimated time to complete this activity
 
Learning Objectives: 1-2 Learning objectives
 
After completing this tutorial, you will be able to…
1. collect soil samples to use for their research project
2. isolate phages from the soil
 
MATERIALS
 
BACKGROUND
Short explanation of background information
 
PROTOCOL
1.  Numbered instructions
* Most steps should have some explanation
 
SUMMARY
* 	Key points and takeaway messages
 
 
Optional elements
Media (Figures, animations, videos)
Admonitions (Warnings, tips, etc.)
 
 

 
MOLECULAR BIOLOGY (Lesson)
 
TITLE: DNA Extraction of Phage samples
 
SUMMARY: 1-2 sentences on the purpose
TIME: Estimated time to complete this activity
 
 
Learning Objectives: 3-4 Learning objectives
 
After completing this lesson, you will be able to…
 
MATERIALS
 
BACKGROUND
Short explanation of background information
Slides or other teaching materials
 
PROTOCOL
1.  Numbered instructions
* Most steps should have some explanation
 
QUESTIONS
* 	Each learning objective should be paired with questions that demonstrate understanding
 
SUMMARY
* 	Key points and takeaway messages
 
 
Optional elements
Media (Figures, animations, videos)
Admonitions (Warnings, tips, etc.)


 
MOLECULAR BIOLOGY (Lesson)
 
TITLE: DNA Extraction of Phage samples
 
SUMMARY: 1-2 sentences on the purpose
TIME: Estimated time to complete this activity
 
 
Learning Objectives: 3-4 Learning objectives
 
After completing this lesson, you will be able to…
 
MATERIALS
 
BACKGROUND
Short explanation of background information
Slides or other teaching materials
 
PROTOCOL
1.  Numbered instructions
* Most steps should have some explanation
 
QUESTIONS
* 	Each learning objective should be paired with questions that demonstrate understanding
 
SUMMARY
* 	Key points and takeaway messages
 
 
Optional elements
Media (Figures, animations, videos)
Admonitions (Warnings, tips, etc.)
 
 
 
BIOINFORMATICS (TUTORIAL)
 
TITLE: Genome assembly
 
SUMMARY: 1-2 sentences on the purpose
TIME: Estimated time to complete this activity
 
Learning Objectives: 1-2 Learning objectives
 
After completing this tutorial, you will be able to…
 
SOFTWARE
* 	Links to software
* 	Container/Docker image (Github)
 
BACKGROUND
Short explanation of background information
 
PROTOCOL
1.  Numbered instructions
* Most steps should have some explanation
 
SUMMARY
* 	Key points and takeaway messages
 
 
Optional elements
Media (Figures, animations, videos)
Admonitions (Warnings, tips, etc.)

 
BIOINFORMATICS (TUTORIAL)
 
TITLE: Genome annotation
 
SUMMARY: 1-2 sentences on the purpose
TIME: Estimated time to complete this activity
 
Learning Objectives: 1-2 Learning objectives
 
After completing this tutorial, you will be able to…
 
SOFTWARE
* 	Links to software
* 	Container/Docker image (Github)
 
BACKGROUND
Short explanation of background information
 
PROTOCOL
1.  Numbered instructions
* Most steps should have some explanation
 
SUMMARY
* 	Key points and takeaway messages
 
 
Optional elements
Media (Figures, animations, videos)
Admonitions (Warnings, tips, etc.)
 
BIOINFORMATICS (TUTORIAL)
 
TITLE: Genome Comparison
 
SUMMARY: 1-2 sentences on the purpose
TIME: Estimated time to complete this activity
 
Learning Objectives: 1-2 Learning objectives
 
After completing this tutorial, you will be able to…
 
SOFTWARE
* 	Links to software
* 	Container/Docker image (Github)
 
BACKGROUND
Short explanation of background information
 
PROTOCOL
1.  Numbered instructions
* Most steps should have some explanation
 
SUMMARY
* 	Key points and takeaway messages
 
 
Optional elements
Media (Figures, animations, videos)
Admonitions (Warnings, tips, etc.)

 BIOINFORMATICS (TUTORIAL)
 
TITLE: Phylogenetics
 
SUMMARY: 1-2 sentences on the purpose
TIME: Estimated time to complete this activity
 
Learning Objectives: 1-2 Learning objectives
 
After completing this tutorial, you will be able to…
 
SOFTWARE
* 	Links to software
* 	Container/Docker image (Github)
 
BACKGROUND
Short explanation of background information
 
PROTOCOL
1.  Numbered instructions
* Most steps should have some explanation
 
SUMMARY
* 	Key points and takeaway messages
 
 
Optional elements
Media (Figures, animations, videos)
Admonitions (Warnings, tips, etc.)

