Typically we highlight web-based tools for our Tips of the Week. But sometimes there’s a tool that has some novel visualizations that we want to note that might require a user to do a download and installation. This week’s tool is one of those–BANDAGE, a Bioinformatics Application for Navigating De novo Assembly Graphs Easily.
I heard about it on twitter, and I was drawn to the paper right away by the visual representation in that figure:
— Stephen Turner (@genetics_blog) July 2, 2015
It happened to come out around the same time I was thinking about the paths used to graphically represent variation data among individuals too. So I had been thinking a lot about ways to show alternate paths of sequence data with graphical representations. And although I don’t do assemblies myself–I focus downstream of that when the data is already refined–it’s useful to think about the challenges of assembling these data sets. And the interest in the tool suggested to me that people who do de novo assemblies might want to hear about this.
The Bandage team has several videos that help to explain the features of their tool. I’ll highlight the overview/introduction here for this weeks Tip of the Week, but if you want to learn more about the details be sure to check out their others.
So have a look at Bandage and see if it helps you to solve de novo assembly issues for your project. Or just think about how others tackle these problems before they get submitted to the databases for everyone’s use. I think people who use data downstream should be aware of the way that the genome assembly folks are faced with the data. I found it really helpful to conceptualize this.
Wick, R., Schultz, M., Zobel, J., & Holt, K. (2015). Bandage: interactive visualization of genome assemblies Bioinformatics DOI: 10.1093/bioinformatics/btv383