Germline sets, or additional data for existing sets, is provided in two CSV files which are uploaded to the site. This repo documents file formats and the process to follow in creating them. It also provides a number of utilities which are designed to simplify data creation and to check the data before upload.
Tag: howto
Gene Tables and Alignments!
This month we’ve added gene tables and alignments to OGRDB. Both can be reached from the Sequences dropdown at the top of every page. Gene Tables list all the sequences in a locus, organised by gene. You can click on the sequence name to see full details of the sequence, including the support we have… Continue reading Gene Tables and Alignments!
OGRDB API v2
The OGRDB API has been upgraded to provide new features: This guide describes the new API. The old API is still available for compatibility with existing scripts.
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
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
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
Preprint on germline set development now available
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.
Using the OGRDB mouse germline sets
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