Is There A Tool To Visualize Sequence Graphs?

Question

[degradator]

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.

[degradator]

Edited my post to not be trinity specific.

[Giovanni M Dall'Olio]

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

Answer 1

[David]

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

[degradator]

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

Answer 2

[VS]

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

[degradator]

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).

Answer 3

[predeus]

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

Answer 4

[predeus]

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