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
Category: OGRDB_News
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
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
Human IG germline sets now available
Germline sets for human IGH, IGK and IGL are now available for download. They are described in a forthcoming publication, “AIRR-C Human IG Reference Sets: curated sets of immunoglobulin heavy and light chain germline genes”, currently available from Biorxiv as a preprint. Our aim with these sets is to provide high-quality, evidenced collections that are… Continue reading Human IG germline sets now available
Downloading germline sets from the command line or API
In this post, we’re going to look briefly at the different ways that you can download germline sets from the command line, or from code. We want to make germline sets on OGRDB as easy to work with as possible, and making them available for download conveniently is an important part of that, so that… Continue reading Downloading germline sets from the command line or API
Germline Set format updates
The JSON format in which germline sets are distributed has been updated (germline sets are also available from OGRDB in FASTA format, but the JSON format provides much richer information). The revised format is compliant with the latest development version of the AIRR schema, which is expected to be released as an update in the… Continue reading Germline Set format updates