Is There A Tool To Visualize Sequence Graphs?
4
1
Entering edit mode
8.5 years ago
degradator ▴ 10

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.

graph sequence tool • 4.6k views
ADD COMMENT
0
Entering edit mode

Edited my post to not be trinity specific.

ADD REPLY
3
Entering edit mode

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

ADD REPLY
2
Entering edit mode
8.5 years ago
David ▴ 740

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 COMMENT
0
Entering edit mode

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 REPLY
2
Entering edit mode
8.5 years ago
VS ▴ 720

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 COMMENT
0
Entering edit mode

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 REPLY
1
Entering edit mode
2.9 years ago
predeus ★ 1.7k

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

ADD COMMENT
1
Entering edit mode
ADD COMMENT

Login before adding your answer.

Traffic: 1711 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6