Hi all,
Until now, our sequencing facility stores the metadata of our single cell sequencing projects/samples in an Excel spreadsheet, which makes automation, data curation and data consistency difficult as it is error prone. For this reason, we would like to use a database to store all project and sample related metadata. The protocols used in the lab should also be linked to it. Some kind of LIMS with the costumizable possibility to store a lot of metadata?
There are many sequencing facilities and I am sure there are good solutions for storing metadata, so I would like to ask you if you know of any good solutions or use a database for metadata yourself? I know we could build our own, but I think we will discover problems that other already have solved.
The metadata we use are for example the title of the project, the sample name, the name of the collaborator, which "tags" (HTO, CMO, ADT) were used, with the associated sequence, where the sequencing data and downstream analyses are stored, the date of sequencing, concenctrations, sequencing platform, etc.
Thank you for any recommendations!
0 answers
No answers yet.
Log in to answer this question.
-
Forum: Building an open-source LIMS project to better understand lab and bioinformatics workflows
written by Eduardo •
-
Job: Permanent Position as Bioinformatician at the National Genomics Infrastructure (Sweden)
written by Matthias Zepper
-
Job: JOB: Data Ontologist - Remote
written by kathy.pearson •
-
Private Database Schema for NGS results storage (Fastq, BAM, VCF...) ?
written by mikizu •
-
Job: System developer at NGI Stockholm Sequencing Facility, SciLifeLab Sweden
written by Phil Ewels
-
Sequence Data Management
written by navela78
-
How to manage a growing library of genome sequences?
written by vladimir.gritsenko
-
Open Source Ngs Database
written by huskerjeff492 •
-
Bio Research-Oriented Project Management Solutions?
written by Adamc
-
Criteria For Calling Genotypes With High Certainty
written by Thomas
I would say the unless you have access to a lot of money for an enterprise LIMS/customization, most everyone rolls something that suits the local work flow. People loath to change what currently works for them. This makes it almost impossible to tailor any off-the-shelf solution to fit your workflow. If you are serious about this then consider getting help from local database experts/interns and see if you can design something "simple" (start with the basic metadata you want to track, do not design for edge cases from get go even though you may be tempted) to get started.
While not for single cell core facilities
sierra(LINK) is one ope-source option.Thanks for the answer and the suggestion to take it into our own hands and keep it simple. That is definitely a consideration. We will also take a closer look at Sierra to see how adaptable it is.