Question: Preferred Tools For Making Analysis Pipeline Flowchart ?
6
gravatar for VS
5.8 years ago by
VS690
USA
VS690 wrote:

Hi,

I want to make a flow diagram representing detailing all the steps of my analyses. One option is to use powerpoint or adobe illustrator but I want to know if there are any tools specifically for making such workflow schemes, Any recommendations by the biostars will be appreciated.

Thanks!

tool • 6.0k views
ADD COMMENTlink modified 3 months ago by shalin30 • written 5.8 years ago by VS690

Thank you everyone for the answers. I have been looking at the tools and so far Dia looks good to me.

ADD REPLYlink written 5.8 years ago by VS690
12
gravatar for Pierre Lindenbaum
5.8 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum114k wrote:

My current NGS workflow uses a Makefile. I wrote a tool parsing the output of make -d --dry-run and generating an input for GEPHI

see my post: http://plindenbaum.blogspot.fr/2012/11/visualizing-dependencies-of-makefile.html

Here is the ouput of an exome analysis ( 16 samples ):

enter image description here

https://twitter.com/yokofakun/status/278086490809040896

For a simple/small graph you can use dot http://graphviz.org/

ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by Pierre Lindenbaum114k
4

I am going to use this in my lecture notes

ADD REPLYlink written 5.8 years ago by Istvan Albert ♦♦ 78k

I think I should delete my answer :D

ADD REPLYlink modified 12 weeks ago • written 5.8 years ago by Medhat8.0k

Hehe, this is awesome.

ADD REPLYlink written 5.8 years ago by Alex Paciorkowski3.3k
6
gravatar for Medhat
5.8 years ago by
Medhat8.0k
Poland
Medhat8.0k wrote:

Hi,

did you try to use visio ? it is Microsoft product it is not free. it is so easy yet so powerful but also here is a list of other tools powerful and easy as visio but it also free 5 Best Free Alternatives To Microsoft Visio

  • OpenOffice/LibreOffice Draw
  • Dia
  • LucidChart
  • Diagramly
  • Pencil Project

    i hope that i was able to help.

ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by Medhat8.0k

I would add "Visual Paradigm for UML - UML tool for software application development". Community edition is free. http://www.visual-paradigm.com/product/vpuml/

ADD REPLYlink written 5.8 years ago by zx87545.7k
3
gravatar for Biomonika (Noolean)
5.8 years ago by
State College, PA, USA
Biomonika (Noolean)3.0k wrote:

I think that Dia (http://projects.gnome.org/dia/) is perfect and easy to use for such task.

ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by Biomonika (Noolean)3.0k

I think Dia is great. But has a new homepage: https://live.gnome.org/Dia

ADD REPLYlink written 5.8 years ago by Daniel Swan13k
3
gravatar for shalin
3.7 years ago by
shalin30
shalin30 wrote:

http://creately.com is another good software for flowcharting. There are many examples and templates for flowcharts in the blog as well. Its a good visio alternative, available for all the platforms as well.

ADD COMMENTlink written 3.7 years ago by shalin30
3
gravatar for Danielk
3.7 years ago by
Danielk550
Karolinska Institutet, Stockholm, Sweden
Danielk550 wrote:

If you use GATK Queue to write your pipeline, you can add the flag `-gv graph-output.dot` on the cli to generate a dotfile (as in dot graph language) that can be converted to a nice PDF or PNG like so: 

dot -Tpng graph-output.dot > graph.png
dot -Tpdf graph-output.dot > graph.pdf

It's great for both visualisation for presentations, and for debugging pipelines. 

ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by Danielk550
2
gravatar for Damian Kao
5.8 years ago by
Damian Kao15k
USA
Damian Kao15k wrote:

These two are pretty good:

https://www.draw.io/

http://drichard.org/mindmaps/

ADD COMMENTlink written 5.8 years ago by Damian Kao15k
2
gravatar for SES
5.8 years ago by
SES8.1k
Vancouver, BC
SES8.1k wrote:

I'd recommend looking at Taverna, which will not only let you document your workflows but you can also run them and monitor the progress. The good thing about that is you can share your workflow with others. (You can also run your workflows programmatically, thereby extending them with some scripting.) Likewise, you can create and run workflows in Galaxy. There is also a project called Tavaxy (citation for that project is here) which will allow you to interchange parts of workflows from Taverna and Galaxy (I haven't used this one because you have to have a cloud account). I know you only asked about making visual representations of workflows, but it may be helpful to see what has already been created with these tools (and even better if you can actually use part of an existing workflow). If you want to keep it real simple and free, I will also recommend Dia for just drawing your workflows.

ADD COMMENTlink written 5.8 years ago by SES8.1k
1
gravatar for Agapow
5.8 years ago by
Agapow270
London, UK
Agapow270 wrote:

There's no single good tool for this sort of this as you may have gathered. All you can ask for is a good flowcharting tool. I'm partial to yEd (http://www.yworks.com/en/productsyedabout.html), which seems to strike a balance between power and ease of use.

ADD COMMENTlink written 5.8 years ago by Agapow270
0
gravatar for shalin
3 months ago by
shalin30
shalin30 wrote:

my recommendation is Creately Flowchart Software for drawing any kind of flowchart. There are 100 of flowchart diagram examples and templates to be used freely. You can quickly create flowcharts using one-click-create feature. It works on all the platforms too, You can even create work flows, process flows and swim lanes with the app.

ADD COMMENTlink written 3 months ago by shalin30
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