Question: Is There A Tool To Visualize Sequence Graphs?
1
gravatar for degradator
6.5 years ago by
degradator10
degradator10 wrote:

I'm looking for a tool that can visualize sequence graphs.

This tool should read a file (e.g. dot file from trinity) and show the sequence graph. Also I want to see information about each sequence in the graph.

Is there any tool that can do such thing?

Thanks in advance!

EDIT

This is the sequence graph trinity creates: trinity sequence graph

I want a tool that makes this graph more informative. Coloring nucleotides, showing sequence length, position, etc.

sequence tool graph • 3.6k views
ADD COMMENTlink modified 7 months ago by predeus1.2k • written 6.5 years ago by degradator10

Edited my post to not be trinity specific.

ADD REPLYlink written 6.5 years ago by degradator10
3

what do you mean exactly with "sequence graph"? Can you find an example from google/images? thanks :-)

ADD REPLYlink written 6.5 years ago by Giovanni M Dall'Olio26k
2
gravatar for David
6.5 years ago by
David730
David730 wrote:

Looking at the documentation of trinity the dot files you are referring to seems to me like regular DOT files that can be plotted with the dot command line software from graphviz.

Install it from here: http://www.graphviz.org/Download..php

Additional documentation: http://www.graphviz.org/Documentation/dotguide.pdf

then open a terminal and type

dot test.dot
ADD COMMENTlink written 6.5 years ago by David730

Thanks. This works, but i want a tool that shows some more information. I should have clarified in my post, sorry. This command makes a pdf of the file:
dot -Tpdf -o test.pdf test.dot

ADD REPLYlink modified 6.5 years ago • written 6.5 years ago by degradator10
2
gravatar for VS
6.5 years ago by
VS710
USA
VS710 wrote:

I am not sure what you mean by "sequence graph" but maybe the ray cloud browser for visualizing de-bruijn graphs is useful for you. Here -- Ray Cloud Broswer and the github source for the same --- Git

ADD COMMENTlink written 6.5 years ago by VS710

Looks very interesting, but not quite what I want. Ray Cloud Browser visualizes de-bruijn graphs (if I understood correctly) but not sequence graphs (see my edited post for a picture).

ADD REPLYlink written 6.5 years ago by degradator10
1
gravatar for predeus
12 months ago by
predeus1.2k
Russia
predeus1.2k wrote:

Old post, but just for the sake of modern searches: Bandage is a very useful modern tool with lots of good functionality

ADD COMMENTlink modified 12 months ago • written 12 months ago by predeus1.2k
1
gravatar for predeus
7 months ago by
predeus1.2k
Russia
predeus1.2k wrote:

And now there's also AGB: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz072/5306331

ADD COMMENTlink written 7 months ago by predeus1.2k
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