Question: Preferred Tools For Making Analysis Pipeline Flowchart ?
6
gravatar for VS
4.6 years ago by
VS670
USA
VS670 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 • 4.7k views
ADD COMMENTlink modified 16 months ago by Biostar ♦♦ 20 • written 4.6 years ago by VS670

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

ADD REPLYlink written 4.6 years ago by VS670
10
gravatar for Pierre Lindenbaum
4.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum98k 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 4.6 years ago • written 4.6 years ago by Pierre Lindenbaum98k
3

I am going to use this in my lecture notes

ADD REPLYlink written 4.6 years ago by Istvan Albert ♦♦ 73k

i think i should delete my answer :D

ADD REPLYlink written 4.6 years ago by Medhat6.9k

Hehe, this is awesome.

ADD REPLYlink written 4.6 years ago by Alex Paciorkowski3.3k
6
gravatar for Medhat
4.6 years ago by
Medhat6.9k
Poland
Medhat6.9k 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 4.6 years ago • written 4.6 years ago by Medhat6.9k

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 4.6 years ago by zx87543.7k
3
gravatar for Biomonika (Noolean)
4.6 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 4.6 years ago • written 4.6 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 4.6 years ago by Daniel Swan13k
3
gravatar for shalin
2.5 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 2.5 years ago by shalin30
3
gravatar for Danielk
2.5 years ago by
Danielk530
Karolinska Institutet, Stockholm, Sweden
Danielk530 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 2.5 years ago • written 2.5 years ago by Danielk530
2
gravatar for Damian Kao
4.6 years ago by
Damian Kao14k
UK
Damian Kao14k wrote:

These two are pretty good:

https://www.draw.io/

http://drichard.org/mindmaps/

ADD COMMENTlink written 4.6 years ago by Damian Kao14k
2
gravatar for SES
4.6 years ago by
SES7.9k
Vancouver, BC
SES7.9k 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 4.6 years ago by SES7.9k
1
gravatar for Agapow
4.6 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 4.6 years ago by Agapow270
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1385 users visited in the last hour