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Whole-genome alignment visualization

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!

cactus maf bigmaf
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updated by SanjidaR_NCBI • SanjidaR_NCBI • written by gubrins gubrins

1 answer

Have you tried IGV?

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

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written by noodle noodle

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

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written by gubrins gubrins

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