Dealing with sequencing data annotations

Question

[kulvait]

Hello,

I am about to assemble pipeline and software for automatic run of QC, aligning, SNP calling etc. I would like to get some standard form of annotating sequencing runs.

The problem is that annotations for different runs typically lives in excel files with non standard structure and it is really hard to even extract names of files from those files since they typically lacks this information.

I would like to have some tool to store annotations with all the file locations and also phenotype information about samples, processing dates etc. in the database. Is there any standard format for this? I found only MINSEQE initiative but I see no tools to support it nor standard column names in databases or annotations.

Thanks, Vojtech.

Answer 1

[mark.ziemann]

I think you are looking for something called a LIMS Laboratory information management system. You might be interested in Sierra, which is open source and free.