GUI framework for sequence data analysis and visulaization

Question

[Pappu]

I am wondering if there is any open source sequence data visualization and data analysis GUI framework preferably in python in which can be easily extended to add custom tools. I am looking for open source alternatives to Geneious or CLC.

The problem is that there are too many bioinformatics tools available. I need a GUI interface where I can easily add custom tools. Thanks.

[h.mon]

Check DNAplotlib.

Answer 1

[Pierre Lindenbaum]

https://usegalaxy.org/

[Pappu]

Galaxy does not seem to have nice interactive data visualization and editing.

[martenson]

Galaxy has:

• charts: https://wiki.galaxyproject.org/Learn/Visualization/Charts
• trackster: http://www.nature.com/nbt/journal/v30/n11/full/nbt.2404.html
• ipython:
• Jupyter (e.g. Rstudio):
• Krona: https://github.com/marbl/Krona/wiki

and much more.

[Pappu]

Sounds cool! Yet not sure about the possibility of interactive editing of data, sequence alignment etc.

[martenson]

iPython and Jupyter are designed for interactive editing

other tools generally work with Galaxy Datasets that you can modify with any other Galaxy tools (including basic text-manipulation ones) See https://usegalaxy.org

Answer 2

[vranckx.katleen]

I think you will get more specific answers if you give more details on what type of visualisations you expect and what kind of data you are working on, as typically, a specific tool is specialised in a specific type of analysis/data. Are you working with sanger sequences, Illumina, PacBio,...; whole genome, prokaryotic, eaukaryotic, metagenome,...

We develop a software called BioNumerics, that is neither open nor free, but it does offer nice visualisations of all types of data (focus is on prokaryotes) and there is a Python editor that allows you to add your own functionality. But this is also the case for CLC and Geneious, so I'm not sure what it is exactly that you are lacking in these softwares?

[Pappu]

Just looking for an open source one to add plugins of softwares I use.

[martenson]

Galaxy visualization plugins: https://wiki.galaxyproject.org/Develop/Visualizations

Biojs to Galaxy: https://github.com/biojs/biojs2galaxy http://biojs.net/