You’ve probably heard of bandage. This handy tool is used to visualize assembly graphs. It helps to show the connections and overlaps in genome assemblies. Pretty cool, huh? Sometimes you may need something different. You might want to add more features or Bandage may not fit with your project. Don’t stress, though! There are many great alternatives available, and I have gathered them for you.
1. Tablet
Consider tablet the most practical tool to view your sequencing data. This is the perfect tool if you want to match your reads with a reference genome rather than piecing assembly graphs together.
Why it’s awesome
- It’s super easy to use (you’ll love it, I promise).
- This software is great for handling large datasets, without making your computer cry.
- You can examine the coverage of each base in detail.
Who it’s for: This is the one to use if you love reference maps and enjoy smooth navigation.
2. IGV
IGV can be compared to a Swiss Army Knife for genome visualization. IGV is similar to Bandage, in that you can zoom into specific areas. However, IGV works on all kinds of data including variant files (VCF), alignments (BAM), and more. It’s a multitasking champion.
Why it’s awesome
- Zoom in and out of your data with super-fast speed.
- You don’t have to stick with a single format. It can handle multiple types of genomic data.
- Ideal for comparing data such as gene variants between samples.
For Whom is it?
IGV has you covered if you need to manage multiple data types, and need an adaptable tool.
3. Gephi
Listen to me on this. Gephi doesn’t qualify as a bioinformatics software. It’s actually a graph-visualization tool. This tool is great if you’re working with incredibly complicated graphs.
Why it’s awesome
- It uses fancy algorithms to organize your graphs in a manner that makes sense.
- You can change the visuals in order to emphasize what is important.
- This is a great tool for handling large, complex datasets.
For Whom is it?
Try Gephi if you are comfortable with graph networks but want to have more control over the visuals.
4. GView
Have you ever drawn a map in circles to help make sense of something? GView works the same way, only for genomes. It is designed to produce high-quality maps that are perfect for large genomes and comparisons.
Why it’s awesome
- Interactive maps are not limited to static, pretty maps.
- Annotations and genome structure? GView allows you to put them together in a way which makes them click.
- This is a great tool for comparing several species simultaneously.
For Whom is it?
It’s a must-have for anyone working on circular genomes, such as bacterial plasmids. It’s also a necessity for comparative genome studies.
5. Cytoscape
Cytoscape is like Gephi’s bioinformatics savvy cousin. It tackles data integration and networks. This tool is a pro when it comes to integrating data, whether you’re looking for gene expressions, interactions between proteins, or assembly results.
Why it’s awesome
- There are tons of plugins that add additional functionality (it is like getting extra levels in a video game).
- Databases and biological resources can be woven into your design.
- Customize it to exactly what you want to show off.
For Whom is it?
Cytoscape can be used to create a neat visual package if you have a lot of layers.
6. REviewer
You’re looking for something new and simple. Reviewer is the perfect solution. It’s about comparing genome assembly arrangements and visualizing them in an easy, lightweight manner.
Why it’s awesome
- The interface is very clean and simple to use.
- It’s available directly from your browser. You don’t need to download anything.
- This study focuses on the comparison of two genome arrangements.
For Whom is it?
This is a great option for those who are new to the game and want to start with the basics.
What to Look for When Choosing the Right Tool
The tool you choose depends on the project. You can use these questions to guide you.
- Do you work with reference genomes, or do you do de novo assembly?
- Do you need multiple genomes to compare?
- Are you interested in learning a tool with broader applications, such as Gephi or Cytoscape
Bioinformatics is a vast field, and the “perfect” tool will be the one that allows you to do your work without making you crazy.
Wrapping it Up
bandage may be a great option for visualizing assembly graphs, but it is not the only one. You have a wide range of options, whether you want to map genomes using GView, explore networks with Cytoscape, Gephi or REviewer or stay web-based.
Try a few and see what works for you. It’s important to make your bioinformatics journey as easy (and fun!) as possible. Enjoy your exploration!
