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.
Tools for working with germline sets
The AIRR-C standard germline sets published in OGRDB use a new naming scheme: please see this poster for details. Because the format of these names may not be compatible with all current pipeline tools, we have released receptor-germline-tools: utilities that can convert to more compatible subgroup-identifier-allele form. We have also updated the FASTA files downloadable… Continue reading Tools for working with germline sets
MiAIRR metadata in VDJbase
VDJbase now provides AIRR-seq study metadata that follows the MiAIRR schema. For those studies that are listed in the iReceptor gateway, the metadata reflects that served by the gateway. For other studies, the metadata provided by VDJbase has been converted to MiAIRR attributes. This means that there are many more columns to choose from on… Continue reading MiAIRR metadata in VDJbase
Further updates to AIRR-seq IGH analysis
The IGH records are now processed with a pipeline that provides improved handling of sequences that are duplicated in the reference set: that is, multiple allele definitions having the same sequence. A bug in OGRDBstats that created incorrect full v-sequence alignments has also been fixed.
First Germline Sets Published on OGRDB
We have published IGHV germline sets for laboratory mouse strains BALB/c and C75BL/6, as recently reported in preprint by Jackson et al.The sets will be curated by the AIRR Community Germline Database Working Group with the aim of maintaining sets that are tuned for use in AIRR-seq, taking advantage of the latest research. We hope… Continue reading First Germline Sets Published on OGRDB
IGH Analysis updated
The analysis of the Human IGH dataset has now been updated to determine novel sequences based on the actual V length inferred by igblast, enabling greater recognition of variation at the 3′ end. To provide greater detail on the analysis, we now provide the commit id of the pipeline version used for analysis in the… Continue reading IGH Analysis updated
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