Data Management Solution For Ngs/Rna-Seq

Question

[Konrad]

Hi,

I would like to know if anyone is aware of an open-source web based data management solution / LIMS that can handle NGS/RNA-Seq data adequately. It should help to organize sequencing data (i.e. raw reads), read mappings and further downstream analyses inside a lab. Maybe there is already something out there that offers proper data models and handy functionalities/visualizations. Otherwise I need to start something from scratch using Django.

Thanks!

Answer 1

[Jeremy Leipzig]

https://www.biostars.org/local/search/page/?q=lims

[Konrad]

Thanks Jeremy. LIMSs were covered in general quite often but as far as I can see there is nothing that supports RNA-Seq besides general data management capabilities. So guess I have to use one of those or write my own application.

Answer 2

[Faheemmitha]

Take a look at bixfile, which happens to be written using Django. It might give you some ideas. I'd be happy to answer questions (faheem at faheem dot info). This is supposedly for handling bioinformatics data, but at the moment the bioinformatics is sketchy to the point of non-existence. Mostly what it does right now is let the user upload files to a directory, and registers the file location to a database. For large files, this is surprisingly difficult to handle with all the corner cases. I don't know if Django is necessarily the best web framework for this, but I doubt if any of the other options are particularly optimized for this sort of thing.