OGRDB now supports Cell Ranger! Specifically, you can use the receptor_utils download tool to download our Human IG sets in a 10x-supported format, and then use Cell Ranger to create a reference set for annotation. Natively, Cell Ranger only annotates at the gene level. Using the OGRDB sets therefore adds a substantial degree of additional… Continue reading Cell Ranger support added
Category: OGRDB
AIRR-C GLDB WG resources
OGRDB is the AIRR Community database of reference sets for IG and TR receptor germline alleles. All sets are freely available for commercial and non-commercial use. Data formats and API conform to AIRR-C’s MiAIRR standards. receptor-utils provides command-line tools for working with OGRDB germline sets. It provides walkthroughs for using OGRDB sets with:– IgBlast– MiXCR… Continue reading AIRR-C GLDB WG resources
Rhesus Macaque IG Germline sets released
The Germline Database Working Group of the AIRR Community is pleased to announce publication on OGRDB of rhesus macaque germline sets covering all three IG loci. These sets include IG sequences from the recent publication in Immunity, “Population-level genomic analysis of immunoglobulin loci variation in rhesus macaques reveals extensive germline diversity” [1], derived from 106… Continue reading Rhesus Macaque IG Germline sets released
Human IGHC set released
We’re pleased to publish the first version of a human IGHC germline set on OGRDB. The set is based on the work of Jana et al., 2025, and contains 105 full-length IGH constant region sequences, derived from long-read genomic sequencing. This work substantially increased the number of published sequences and revealed significant polymorphism and population… Continue reading Human IGHC set released
Explanation of germline set formats
This article gives a brief explanation of the different germline set formats available from OGRDB. Recommended for AIRR-seq Analysis The sets available from the Download pages are tuned for AIRR-seq analysis. In particular, duplicate sequences are removed and sequences inferred from transcripts are extended to their likely full length, as inferred from other alleles of… Continue reading Explanation of germline set formats
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. To download germline sets in FASTA or AIRR-C format, just press the Download Germline Sets button on the home page, and select the species you require. To download full details of… Continue reading Downloading OGRDB Data
Introduction to OGRDB
Introduction to OGRDB In recent years it has become possible to sequence immune receptor repertoires (immunoglobulins and T cell receptors) at great depth. The accurate analysis of these repertoires requires a comprehensive understanding of the germline genes that give rise to the repertoire through V(D)J gene recombination. Even for well-studied species such as humans and… Continue reading Introduction to OGRDB
Submitting inferences to OGRDB
If you have identified previously undocumented alleles in AIRR-Seq repertoires, we invite you to submit them to OGRDB for review and possible inclusion in published germline reference sets. At present, you can submit human IG or TR V-sequences for consideration. We hope to extend this to cover more species and loci soon. Qualification criteria To… Continue reading Submitting inferences to OGRDB
Creating a select set
A select set is a set of reads taken from a single repertoire that directly support a specific inference. In outline, the process to create the set is as follows: For a paired-end-read dataset, merge all paired-end reads Align reads to the inferred allele reference Filter the output to an identity of at least 96%… Continue reading Creating a select set
OGRDB – Depositing records in NIH repositories
At the end of this deposition process, NCBI will contain two types of record for use in your submission: A sequence record for each inferred sequence you intend to submit. One or more select sets for each inferred sequence. The deposition process for each type is detailed below. As sequence records refer to select sets,… Continue reading OGRDB – Depositing records in NIH repositories