Start with demultiplexed sequencing reads from an Illumina or Oxford Nanopore Technologies sequencer and finish with high quality genomes submitted to public repositories!
flowchart LR
A[Demulitplexed\nReads] --> B[IRMA\nassembly]
B --> C[DAIS-Ribosome\nannotation]
C --> D{Quality\nAssessment}
D --> E[SeqSender]
E --> F[(GISAID)]
E --> G[(NCBI)]
style A fill:#153b60,color:#FFFFFF,stroke:#333,stroke-width:5px
style B fill:#89b342,color:#000000,stroke:#333,stroke-width:5px
style C fill:#89b342,color:#000000,stroke:#333,stroke-width:5px
style D fill:#06a4d5,color:#000000,stroke-width:10px
style E fill:#89b342,color:#000000,stroke:#333,stroke-width:5px
style F fill:#e3e3e2,color:#000000,stroke:#333,stroke-width:5px
style G fill:#e3e3e2,color:#000000,stroke:#333,stroke-width:5px
- A minimum of 16GB of memory is required. >=32GB is recommended.
- A minimum of 8 CPU cores is recommended.
- Administrative privileges are required on a Windows operating system to run linux.
- A linux operating system is required.
You can get a full linux environment using Windows Subsystem for Linux, or WSL. The second version of WSL is WSL2 and is the recommended version to use.
- Click the Windows Logo in the bottom left corner of the screen and type "powershell"
- Type "wsl" and hit Enter:
which will change your prompt to:
C:\Users\username> wsl
but with your username@computername:username$
-
Make a data directory somewhere, ie. right-click the desktop:
-
Navigate to your data directory by copying and pasting the following command into Command Prompt
cd /mnt/c/Users/$(whoami)/Desktop/data # This assumes that when you set up WSL2 you made your USERNAME the same name as you use to log in to Windows. If not, replace "$(whoami)" with that username.
Docker allows you to run software inside an isolated "container image" on your computer with all of that application's needed dependencies. Make sure to install the version for your operating system. Here we are assuming Windows.
We will use BioEdit to look at consensus sequences.
and then