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.
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
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.
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
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
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.
We welcome submissions of previously undocumented alleles of human receptor genes. The Submission Guide explains the process, which involves deposition of sequences and sequence sets in NIH or ENA repositories. Your submission will be reviewed by AIRR‘s Inferred Allele Review Committee, and, if there is sufficient evidence, the sequence will be published on this site… Continue reading IARC Submission Guide Updated
OGRDB is now accepting V- and J- sequence inferences from the human BCR light and heavy chain. Analysis scripts and submission pages have been updated accordingly.