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 .

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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.

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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.

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

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New inferred sequences accepted by IMGT

A new batch of inferred receptor sequences, submitted for review through OGRDB, has been accepted by IMGT and should be added to their reference sets shortly. This batch included the first IGK and IGL alleles. We have now affirmed a total of 32 sequences, details of which can be found on the Sequences page.

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