Biostar Beta. Not for public use.
Modern software for whole genome alignment visualization
4
Entering edit mode
16 months ago
predeus ♦ 1.1k
Russia

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
1
Entering edit mode

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
1
Entering edit mode

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
0
Entering edit mode

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

ADD REPLYlink
0
Entering edit mode

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

ADD REPLYlink
0
Entering edit mode

Did you find a good browser to visualize 2 or more genomes + other tracks?

ADD REPLYlink
0
Entering edit mode

Nothing outside what was mentioned here, no.

This tool was useful: https://dnanexus.github.io/dot/

it uses Nucmer alignments and creates a pretty useful visualization.

ADD REPLYlink
0
Entering edit mode

Did you reach any conclusions about a supported tool to do dynamic comparisons of multiple genomes? I am interested in genomes around 1.5 Gbases.

ADD REPLYlink
0
Entering edit mode

Hello Gina,

I came to conclusion that Dot tool mentioned above is very useful for a large-scale overview. Also, ACT, ancient as it is, worked quite well with the bacterial genomes I had to compare with annotation. But that might be too much for 1.5 Gb genomes. That's about it.

ADD REPLYlink
5
Entering edit mode
6 months ago
VIB, Ghent, Belgium

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

ADD COMMENTlink
0
Entering edit mode

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

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

ADD REPLYlink
4
Entering edit mode
18 months ago
Seattle, WA USA

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
1
Entering edit mode
15 months ago
Belgium

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

ADD COMMENTlink
0
Entering edit mode

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
1
Entering edit mode

MUMmer 4 is in the works:

https://github.com/mummer4/mummer

ADD REPLYlink
0
Entering edit mode

Ah, thank you. This is very neat.

ADD REPLYlink
1
Entering edit mode
20 months ago
Hussain Ather • 920
National Institutes of Health, Bethesda…

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

ADD COMMENTlink
0
Entering edit mode

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
1
Entering edit mode
17 months ago
h.mon 25k
Brazil

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
0
Entering edit mode

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
1
Entering edit mode
16 months ago
SMK ♦ 1.3k
Ghent, Belgium

CrossBrowse looks nice (biorxiv), although I failed to render gene models for my data... But the author is active at this moment (response to issue), perhaps we can all make it better. :-)

enter image description here

If you aim for visualizing variations (but from read alignment not genome alignment which you're mentioning), Sequence Tube Maps (interactive) might be a good idea:

enter image description here

Hope these help.

ADD COMMENTlink
0
Entering edit mode
2.5 years ago
tianleivv • 20

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

ADD COMMENTlink
0
Entering edit mode

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

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.3.1