Germline sets for human IGH, IGK and IGL are now available for download. They are described in a forthcoming publication, “AIRR-C Human IG Reference Sets: curated sets of immunoglobulin heavy and light chain germline genes”, currently available from Biorxiv as a preprint. Our aim with these sets is to provide high-quality, evidenced collections that are… Continue reading Human IG germline sets now available
Human genomic IGH data now available
A set of ~150 human IGH loci from diverse backgrounds is now available. The data is taken from Rodriguez, Safonova, Silver, Shields, et al. 2023. ‘Genetic Variation in the Immunoglobulin Heavy Chain Locus Shapes the Human Antibody Repertoire’. The data presented here was taken from IGenotyper haplotyped assemblies, processed by the VDJbase automated pipeline. Analysis… Continue reading Human genomic IGH data now available
Downloading germline sets from the command line or API
In this post, we’re going to look briefly at the different ways that you can download germline sets from the command line, or from code. We want to make germline sets on OGRDB as easy to work with as possible, and making them available for download conveniently is an important part of that, so that… Continue reading Downloading germline sets from the command line or API
Germline Set format updates
The JSON format in which germline sets are distributed has been updated (germline sets are also available from OGRDB in FASTA format, but the JSON format provides much richer information). The revised format is compliant with the latest development version of the AIRR schema, which is expected to be released as an update in the… Continue reading Germline Set format updates
Human genomic IGL data now available
Human IGL genomic assemblies are now available for browsing. The data is taken from Gibson, W.S., Rodriguez, O.L., Shields, K. et al. Characterization of the immunoglobulin lambda chain locus from diverse populations reveals extensive genetic variation. Genes Immun 24, 21–31 (2023).
Preprint on germline set development now available
The AIRR Community has recently published a preprint on the community development of IG and TR germline sets. This sets out the principles and approach being followed for the development and publication of germline sets on OGRDB, which we hope will gain wider traction in the community as a whole.
Using the OGRDB mouse germline sets
For many analyses, it is important to annotate AIRR-seq repertoires with an accurate and comprehensive germline set. As an example, determination of the overall mutation rate of a repertoire may give misleading results if frequently-expressed sequences are omitted. Likewise, many methods of clonal assignment require an accurate determination of the germline. The IG loci of… Continue reading Using the OGRDB mouse germline sets
Using the VDJbase REST API
The REST API allows you to access VDJbase programatically, which can be useful if you want to incorporate data into your own systems, and keep it up-to-date. All communication between the VDJbase client in the browser and the VDJbase server is via the API: any data you see in the browser has been provided over… Continue reading Using the VDJbase REST API
Downloading OGRDB Data
OGRDB provides facilities on various pages to download key items of data. Some tables also provide buttons to download in CSV or Excel format. The entire database is archived periodically at Zenodo.org. The latest version is always available at https://doi.org/10.5281/zenodo.7115762 .
Germline sets now have DOIs
Germline sets on OGRDB are copied to Zenodo.org for long-term security and have DOIs issued by Zenodo which you will see on the Germline Sets pages. The DOI is updated with each version: you can provide the DOI for the version used in your research as a permanent link to the set.