Beginner Guide to Bacteriophage Genome Assembly 1. Introduction

The tutorial written by Lucy is an excellent starting point. For those looking for a more detail there is a step by step tutorial here, that was published in the PHAGE journal. With a full list of commands to follow here . With a very useful overview of all steps in the paper of Turner et al, worth reading before starting assembly/annotation.

1. Introduction

What is genome assembly? Why do it?

Genome assembly is using DNA sequencing and bioinformatics and previously published databases and genomes to find out the genome of your phage. Getting this information for your new phage allows you to explore its genetics and compare it to other published phage genomes, of which many can be found at GenBank.

How to assemble a genome?

Your bacteriophage needs to be purified and bulked out, so DNA can be extracted. This DNA sample can be sent for sequencing (using a variety of sequencing techniques), and sequencing data files are received after this has been completed. Many different bioinformatics programs can be used to understand this sequencing information and assemble the new genome from it.

Before you start:

I am using a Mac laptop, and most of the programs are run using Mac Command Line, also called Terminal, through the Bash shell. Terminal is another way of controlling computer programs and files themselves as well as clicking on them through Finder on a Mac. I use the words terminal and bash to mean the same thing; the program and language you use to control files and run some programs on a mac. Bash is like a simple programming language, and you can learn the basics needed in a short time using guides on the internet, I was using this one:

Also I’m logged onto the Millardlab server, as you can sometimes see in my codes or screenshots.

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