Question: Data Management System For Bioinformatics?
4
gravatar for Panos
3.7 years ago by
Panos1.5k
Geneva, Switzerland
Panos1.5k 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!

• 1.9k views
ADD COMMENTlink modified 3.7 years ago by Pierre Lindenbaum98k • written 3.7 years ago by Panos1.5k
4
gravatar for Istvan Albert
3.7 years ago by
Istvan Albert ♦♦ 73k
University Park, USA
Istvan Albert ♦♦ 73k 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 COMMENTlink modified 3.7 years ago • written 3.7 years ago by Istvan Albert ♦♦ 73k
2

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 REPLYlink written 3.7 years ago by Panos1.5k
2
gravatar for Ying W
3.7 years ago by
Ying W3.6k
South San Francisco, CA
Ying W3.6k 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 COMMENTlink modified 3.7 years ago by Istvan Albert ♦♦ 73k • written 3.7 years ago by Ying W3.6k

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

ADD REPLYlink written 3.7 years ago by Panos1.5k
2
gravatar for Pierre Lindenbaum
3.7 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum98k wrote:

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

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ADD COMMENTlink written 3.7 years ago by Pierre Lindenbaum98k

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 REPLYlink written 3.7 years ago by Panos1.5k
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