SEA-PHAGES | Circular Genome Visualization

Link to this post \| posted 06 Oct, 2021 23:45
cellokiwi	Hi, I was wondering if anyone knows of a good program/tool to construct circular diagrams of our genomes (given that they circularize almost immediately inside the host)? I'm wanting to relate gene expression data to location on the chromosome. Thanks in advance for your help!

Link to this post \| posted 11 Mar, 2022 14:51
edgingtonn1	Here is a powerful program, but there is a learning curve! http://circos.ca Here someone has tried to make it easier with a Circos web interface This one looks nice, but costs money. Best, -Nick Cohort IV Southern Connecticut State University 501 Crescent St. Department of Biology, SCI 311E New Haven, CT 06515

Link to this post \| posted 13 Mar, 2022 22:11
cdshaffer	According to this page: https://biostar.usegalaxy.org/p/28273/ The Galaxy instance at Texas A&M has a circos wrapper as well as other graphics methods. The good news is that Galaxy is a web based graphical system for bioinformatic analysis and there is no charge. The bad news is there is still a non-trival learning curve. Galaxy is a really nice middle ground for doing bioinformatics, and the Texas A&M galaxy instance is specifically geared to phage analysis. So, it might be worth considering, but if you have never used Galaxy you are going to need to commit a non-trivial amount of time just to train on Galaxy. I have used Galaxy and think it is one of the best web based systems for complex computational workflows, however, some tools work better than others when implemented in Galaxy and since I have never used that Circos wrapper, I have no idea how good it is. So if you don't know Galaxy there could be a considerable investment in time only to find out the wrapper really doesn't give you what you are looking for. On the other hand Galaxy is a pretty good system to learn if you are looking to dive deeper into bioinformatics and still keep everything in a graphical, web-based format where you don't have to worry about command line, package management, and installation.

Link to this post | posted 13 Mar, 2022 22:11

cdshaffer

According to this page: https://biostar.usegalaxy.org/p/28273/
The Galaxy instance at Texas A&M has a circos wrapper as well as other graphics methods.
The good news is that Galaxy is a web based graphical system for bioinformatic analysis and there is no charge. The bad news is there is still a non-trival learning curve. Galaxy is a really nice middle ground for doing bioinformatics, and the Texas A&M galaxy instance is specifically geared to phage analysis.

So, it might be worth considering, but if you have never used Galaxy you are going to need to commit a non-trivial amount of time just to train on Galaxy. I have used Galaxy and think it is one of the best web based systems for complex computational workflows, however, some tools work better than others when implemented in Galaxy and since I have never used that Circos wrapper, I have no idea how good it is. So if you don't know Galaxy there could be a considerable investment in time only to find out the wrapper really doesn't give you what you are looking for.

On the other hand Galaxy is a pretty good system to learn if you are looking to dive deeper into bioinformatics and still keep everything in a graphical, web-based format where you don't have to worry about command line, package management, and installation.

Recent Activity

Circular Genome Visualization