Please read our update article in Nucleic Acids Research to learn about new features in OGRDB and VDJbase, and plans for the future. William D Lees, Ayelet Peres, Vered Klein, Naama Amos, Uddalok Jana, Eric Engelbrecht, Zachary Vanwinkle, Yaniv Malach, Thomas Konstantinovsky, Pazit Polak, Corey T Watson, Gur Yaari, The current landscape of adaptive immune… Continue reading New publication
Author: william
OGRDB Outage
OGRDB has been down since Saturday 25th October. I am very sorry for the outage, which has been caused by an issue with the Domain Naming System (DNS) record for the site. The issue is under investigation by administrators at the AIRR Community and The Antibody Society. Please be assured that we are doing everything… Continue reading OGRDB Outage
Uploading germline sets to OGRDB
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.
Contributing germline sets to OGRB
We welcome submissions of germline sets for new species, and new sequences for existing species. Under our overall policy, expressed in the name of the site, contributions must be free for anyone to use. OGRDB is structured to allow individuals or groups to manage the sets that they provide, and we hope that they will… Continue reading Contributing germline sets to OGRB
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!
Website updated
We have redesigned the front page and added a new help page which brings together all information on how to use OGRDB. Other pages have been restyled to make them simpler and easier to use. We hope you will enjoy the new site. If there are any problems, please let us know by using the… Continue reading Website updated
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.
Genomic Data Upgraded
We have added additional annotated human loci, taking the overall total to 867. The new annotations are described in two studies: – Jana et al., “The human immunoglobulin heavy chain constant gene locus is enriched for large complex structural variants and coding polymorphisms that vary in frequency among human populations” (preprint). IGHC is represented in… Continue reading Genomic Data Upgraded
AIRR-Seq Data Upgraded: Repertoires downloadable!
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