Whole-genome alignment visualization

Question

[gubrins]

Hi all,

I am using Cactus to align whole genome references and I obtained the hal output. After that, I converted in both maf and bigmaf, but I am struggling in finding a tool to visualize it. I want to compare several regions that present tandem repeats, so ideally I would like to zoom in those regions. Any suggestions?

Thanks in advance!

[SanjidaR_NCBI]

HI! What a coincidence! We're building a viewer at NCBI for whole genome alignments (in MAF/bigMAF). We'd love to talk to you about how you'd best like to visualize your data.

Can you please go here and enter your contact information, and we'll reach out to you soon. https://nlmenterprise.co1.qualtrics.com/jfe/form/SV_5iL6W3r2A7vY52R?ncbi_app=CGV&Source=Content_Request_Link

Thank you!

Answer 1

[noodle]

Have you tried IGV?

https://igv.org/web/release/2.11.2/examples/maf-tcga.html

[gubrins]

Hi, I don't want to visualize Mutation Annotation Format but Multiple Alignment Format, sorry for the confusion. I will give a try to IGV though