Data Management System For Bioinformatics?

Question: Data Management System For Bioinformatics?

5.3 years ago by

Panos • 1.7k

Geneva, Switzerland

Panos • 1.7k wrote:

We're planning to do a great deal of Illumina sequencing (several insects) in our lab and I was looking at data management systems that will be able to handle all this data (raw reads, assemblies, annotations, etc). From what I've found so far it looks like the Sequence Retrieval System is doing exactly what I want, but I'm a bit skeptical since EBI retired it. So does anyone know other data management systems like SRS? Is SRS still be free for academic use?

Thanks!

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modified 5.3 years ago by Pierre Lindenbaum ♦ 119k • written 5.3 years ago by Panos • 1.7k

5.3 years ago by

Istvan Albert ♦♦ 80k

University Park, USA

Istvan Albert ♦♦ 80k wrote:

I for one think that raw reads should not be stored in a database, it is just not worth the effort and overhead for designing such a system.

The next problem is also thorny, what does it really mean to handle assemblies and annotations. The questions one might want to query for are very open ended and most solutions cannot possibly address all the ways people use the data.

What I would do is establish a data sharing solution around a visualization tool like IGV or IGB. Set up a private data server that collaborators can access and use that to explore the data.

ADD COMMENT • link modified 5.3 years ago • written 5.3 years ago by Istvan Albert ♦♦ 80k

Thanks for the input!

I didn't mean to add each individual read in the database! I just want to be able to download the fastq files of each run. As for the assembly/annotation handling, what I want is to be able to keep, for example, different assembly versions (eg uncorrected and corrected versions), or to be able to extract all protein sequences of the annotated genes that match some particular criteria. I also don't necessarily need a visualization of the genomes.

ADD REPLY • link written 5.3 years ago by Panos • 1.7k

5.3 years ago by

Ying W • 3.9k

South San Francisco, CA

Ying W • 3.9k wrote:

Here is a previous post Data management solution for NGS/RNA-Seq from a couple years back as well as a post on Is there a LIMS that doesn't suck? also from a couple years back.

If you end up deciding to just manage the files yourself, you might want to take a look at How do you manage your files & directories for your projects ?

ADD COMMENT • link modified 5.3 years ago by Istvan Albert ♦♦ 80k • written 5.3 years ago by Ying W • 3.9k

Thanks for mentioning those posts Ying. I hadn't seen the one about LIMS.

ADD REPLY • link written 5.2 years ago by Panos • 1.7k

5.3 years ago by

Pierre Lindenbaum ♦ 119k

France/Nantes/Institut du Thorax - INSERM UMR1087

Pierre Lindenbaum ♦ 119k wrote:

have a look at miso: http://www.tgac.ac.uk/miso/

@BioMickWatson @seandavis12 interesting ! I'll have a look http://t.co/mdlGc8TU #lims #ngs
— Pierre Lindenbaum (@yokofakun) September 19, 2012

ADD COMMENT • link written 5.3 years ago by Pierre Lindenbaum ♦ 119k

I think that's a good solution for managing the sequencing data, although it doesn't look like it can manage assemblies or annotation of that data. Thanks Pierre!

ADD REPLY • link written 5.2 years ago by Panos • 1.7k

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