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I've been looking for a program that allows me to visualize pangenomes efficiently and it has been very difficult find satisfactory documentation about large pangenome's visualization tools since most of them are related to prokaryotic genomes (which are smaller size) and/or chunks of eukaryotic genomes to study specific haplotypes. My pangenome has these characteristics:

nodes   18424540
edges   24616683
length  1069101379

My objective is to be able to get an image of the full pangenome or one for each chromosome, from which has to be possible to interpret approximatevly its structure and where significant divergence between the genome sequences is found.

So far the programs I have been using were not able to give a meaningful image of the eukaryotic pangenome in question.

I come here to ask if anyone has found him/herself in this situation before, and if you manage to find a solution or even a compromise to still be able to have an idea of its structure indirectly, it would be very much of help for me!

Thank you in advance

My pangenome has been created following the Cactus pipeline step-by-step (skipping the optional 3rd step).

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the cactus docs talk about visualization here https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md#visualization

I also collect visualization tools and these are the ones i have tagged as "graph" https://cmdcolin.github.io/awesome-genome-visualization/?language=&tag=Graph&platform=&latest=true and ones i have tagged as "pangenome" https://cmdcolin.github.io/awesome-genome-visualization/?language=&tag=Pangenome&platform=&latest=true

I see specifically that you refer to conservation. panagram was a tool that was presented that actually does a very nice way of showing conservation by k-mers. it is not graph based, but k-mer based https://github.com/kjenike/panagram (presentation https://www.dropbox.com/s/g7snjgr8bs6c2uj/2023.01.17.Panagram.pdf). other tools you see on posters a lot also include syri/plotsr https://schneebergerlab.github.io/syri/ and GENESPACE.

this is also of course a relatively new field, so, you might also make your own tools/visualizations for the purpose (and share them back with us!)

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One additional option that I'll mention is anvi'o (scroll down to the figures to see if it's something you might be interested in https://merenlab.org/2016/11/08/pangenomics-v2/ ).

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    $\begingroup$ I've been spending some time to go through anvi'o documentation and it seems a very interesting tool but not exactly useful for my purpose. I want to focus on the visualization of a pangenome constructed with the cactus pipeline that is able to create a single pangenome graph and my aim is to use it as reference for assembly of other organisms of the same specie. Therefore I just need to visualize its structure to better understand if there are big issues with it before starting evaluating the mapping performances. As far as I understood anvi'o focus on comparative genomics. But thank you! $\endgroup$
    – AIsaac
    Commented May 29 at 9:08

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