Question: Modern software for whole genome alignment visualization
1
gravatar for predeus
3 months ago by
predeus560
Russia
predeus560 wrote:

Hello all,

I was wondering if there are any modern tools for visualization of whole-genome alignment, with ability to add annotation, and maybe extract variants? I've tried Mauve and Harvest so far, but they seem pretty abandoned and work quite poorly.

Are there any modern projects you can recommend? Surely with more and more genomes becoming available, there should be some tools to compare them? I am looking for something tailored to bacterial comparison, ideally, but any leads are welcome.

ADD COMMENTlink modified 3 months ago by h.mon15k • written 3 months ago by predeus560

I think there's a separation of concerns issue here OP. Genome browsers are typically responsible for loading BAM, fasta, and BED annotations, maybe vcfs. They are a data exploration application.

Ability to extract variants... you mean predict from the BAM files? Or you mean export the loaded vcfs? If you're talking about the former, as developers, we should keep the mathematics/algorithms separate from visualization applications such that we can iterate rapidly on both UI and server-side methods, rather than rely on one large monolithic application for everything. Does this make sense?

ADD REPLYlink written 3 months ago by mrals8910
1

Maybe I did not make myself sufficiently clear. I have no problem choosing a classical genome browser (with one reference and one annotation) to view and analyze coverage, annotation, etc. Variant/coverage analysis for typical use cases (short reads aligned to a reference) are no problem as well.

I do, however, have a problem with similar software for comparison of 2 or more genomes. Basically, I was looking for more modern and more feature-rich versions of Mauve or ACT.

ADD REPLYlink written 3 months ago by predeus560

Compare in what way, sir? Are you looking at rearrangements? CNVs? Or are you interested in homology and sequence features?

ADD REPLYlink written 3 months ago by mrals8910

SNPs and indels with annotations (silent/missense/nonsense, frameshift/in-frame), for example.

ADD REPLYlink written 3 months ago by predeus560
3
gravatar for lieven.sterck
3 months ago by
lieven.sterck1.7k
Belgium, Ghent, VIB
lieven.sterck1.7k wrote:

someone recently pointed me to this one: D-Genies . Haven't tried it myself though.

ADD COMMENTlink modified 3 months ago • written 3 months ago by lieven.sterck1.7k

ha, that is a very creative use of minimap2 :)

at least there's a js visualization, worth a shot. Thank you.

ADD REPLYlink written 3 months ago by predeus560
2
gravatar for Alex Reynolds
3 months ago by
Alex Reynolds24k
Seattle, WA USA
Alex Reynolds24k wrote:

There's HiGlass, which is more for Hi-C datasets at this point, but a dotplot is effectively a heatmap and so may be usable for what you're doing.

It uses a "Google Maps"-like approach of scaling datasets at different resolutions, and so zooming in and out at different scales happens very quickly:

ADD COMMENTlink written 3 months ago by Alex Reynolds24k
1
gravatar for WouterDeCoster
3 months ago by
Belgium
WouterDeCoster29k wrote:

That sounds like a job for mummer http://mummer.sourceforge.net/

ADD COMMENTlink written 3 months ago by WouterDeCoster29k

Last update on the code is in 2011, publications are from 2000-2004. Is it really still relevant? Visualizations look pretty horrible too (by modern standards of course).

ADD REPLYlink written 3 months ago by predeus560
1

MUMmer 4 is in the works:

https://github.com/mummer4/mummer

ADD REPLYlink written 3 months ago by h.mon15k

Ah, thank you. This is very neat.

ADD REPLYlink written 3 months ago by predeus560
1
gravatar for Hussain Ather
3 months ago by
Hussain Ather860
National Institutes of Health, Bethesda, MD
Hussain Ather860 wrote:

Mauve works too. http://darlinglab.org/mauve/mauve.html

ADD COMMENTlink written 3 months ago by Hussain Ather860

yes, I did mention it in the original post... it's very poorly maintained, it seems. And since it's a Java jar, if it fails, there's no real way to debug it - you just have to accept it.

ADD REPLYlink written 3 months ago by predeus560
1
gravatar for h.mon
3 months ago by
h.mon15k
Brazil
h.mon15k wrote:

I don't know of any software that meet all your needs, but you may try anvi'o and Artemis.

I've read somewhere (don't have the link) the The NCBI Genome Workbench may do what you want. I've never used it, though.

edit: web genome browsers (UCSC, GBrowse, JBrowse) are quite powerful, extensible and flexible, but probably not easy to set up.

ADD COMMENTlink modified 3 months ago • written 3 months ago by h.mon15k

Artemis Comparison Tool (ACT) is the tool related to Artemis, that does multi-genome visualization. It's very ancient and bad though, just painfully so.

Thank you for he anvi'o link, I will check it out though.

ADD REPLYlink written 3 months ago by predeus560
0
gravatar for tianleivv
3 months ago by
tianleivv0
tianleivv0 wrote:

Have you tried Circos (http://circos.ca/)?

ADD COMMENTlink written 3 months ago by tianleivv0

yes, of course. I think I should have specified that I was looking for a dynamic visualization - sort of like genome browser, but for 2 (or possibly more) genomes.

ADD REPLYlink written 3 months ago by predeus560
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