We are pleased to announce a major upgrade to human AIRR-seq data on VDJbase. We have added approximately 1000 new repertoires, bringing the total to 2,345. For improved consistency and reproducibility, all repertoires have been processed with a new pipeline, processing from source reads wherever possible. IG AIRR-seq is now annotated with the AIRR-C Reference… Continue reading AIRR-Seq Data Upgraded: Repertoires downloadable!
Additional support for germline sets
We have created step-by-step walk-throughs showing how to use the AIRR-C germline sets with local installations of IgBLAST and MiXCR. These tools make use of download_germline_set, which is a powerful command-line utility which can be used to download sets in various formats, and explore the sets and versions available in OGRDB. It can even create… Continue reading Additional support for germline sets
Mouse IG Reference Sets Updated
Fixes have been made to two mouse reference sets. In C57BL/6 IGH, a stray character in the coding sequence for IGHV-KAOG has been removed. There are no other changes to this set. In PWD/PhJ IGH, the delineation j_cdr3_end has been corrected. There are no other changes in this set, and coding sequences are unchanged.
Human IG Reference Sets Updated
The human IG reference sets on OGRDB have been updated and carry new versions, but no coding sequences are affected. The updates add longer gene sequences for many light-chain alleles, allowing better characterisation of leader and RSS. Delineations of CDRs and other features have been reviewed and fixed in some cases. The changes made are… Continue reading Human IG Reference Sets Updated
Genomic data extended
Genomic data has been extended to include 36 human IGK samples from Engelbrecht, Rodriguez, Shields et al., 2024. We have replaced the 22 human IGL samples published in Gibson, Rodriguez, Shields et al., 2022 with 200 that have been processed with more accurate sequencing and pipelines than were available for that study. The IGL and… Continue reading Genomic data extended
Read support for genomic alleles
The annotation file for a genomic sample can be found by clicking on the folder icon in the VDJbase Samples tab. This file lists the alleles that were determined from the sample. In the Genes tab of VDJbase, the ‘Max cov sample’ column shows, for each allele, the sample in which it was found with… Continue reading Read support for genomic alleles
OGRDB Updated
OGRDB has been updated to use binomial (latin) species names instead of colloquial names. The former names can still be used in calls to fetch germline sets, which I hope will prevent automated scripts from breaking, but if you do have problems please try substituting, for example, “Homo sapiens” for “Human”. This turned out to… Continue reading OGRDB Updated
Collaboration Opportunities
OGRDB and VDJbase are part of the AIRR Knowledge Commons project – bringing together immune repertoires from the AIRR Data Commons, epitopes from IEDB, receptor germline analysis from OGRDB and VDJbase with other emerging datasets. We are actively seeking collaborators whose projects will drive use cases and demonstrate the utility of bringing these various sources… Continue reading Collaboration Opportunities
Novel Allele Submission Process Simplified
Following an IARC decision in December 2023, the submission process for inferred novel alleles has been simplified. Previously, it was necessary to deposit the sequence of each inferred allele in GenBank or ENA, and it was usually necessary to accompany this with an extracted set of reads from the repertoire that provided explicit support for… Continue reading Novel Allele Submission Process Simplified
Germline Databases, or adventures into the allelic underworld
If you are interested in receptor germlines, you might enjoy this On-AIRR podcast with Corey Watson and William Lees, hosted by Ulrik Stervbo and Zhaoqing Ding. “In this episode we talk about the recent work by the Germline Database Working Group of the AIRR-Community. The accuracy of V and J gene segment assignment improves with… Continue reading Germline Databases, or adventures into the allelic underworld