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.
Author: william
Submitting inferences to OGRDB
If you have identified previously undocumented alleles in AIRR-Seq repertoires, we invite you to submit them to OGRDB for review and possible inclusion in published germline reference sets. At present, you can submit human IG or TR V-sequences for consideration. We hope to extend this to cover more species and loci soon. Qualification criteria To… Continue reading Submitting inferences to OGRDB
Creating a select set
A select set is a set of reads taken from a single repertoire that directly support a specific inference. In outline, the process to create the set is as follows: For a paired-end-read dataset, merge all paired-end reads Align reads to the inferred allele reference Filter the output to an identity of at least 96%… Continue reading Creating a select set
OGRDB – Depositing records in NIH repositories
At the end of this deposition process, NCBI will contain two types of record for use in your submission: A sequence record for each inferred sequence you intend to submit. One or more select sets for each inferred sequence. The deposition process for each type is detailed below. As sequence records refer to select sets,… Continue reading OGRDB – Depositing records in NIH repositories
OGRDB – Depositing records in ENA repositories
At the end of this deposition process, ENA will contain two types of record for use in your submission: A sequence record for each inferred sequence you intend to submit. One or more select sets for each inferred sequence. The deposition process for each type is detailed below. As sequence records refer to select sets,… Continue reading OGRDB – Depositing records in ENA repositories
Creating an OGRDB Submission
Pre-Requisites Before submitting inferred sequences with OGRDB, you should have run OGRDBstats on each repertoire: otherwise, please follow steps in the overall submission process before continuing. Having run OGRDBstats, you should have output files (pdf and csv) for each repertoire from which inferences have been derived. The project should be deposited in a long-term repository,… Continue reading Creating an OGRDB Submission
IARC Submission Guide Updated
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
Genomic data in VDJbase
Genomic data is organised into ‘genomic sets’: typically a genomic set will contain data relating to a single locus of a species. At the moment, VDJbase holds genomic data for Rhesus Macaque but not for Human: when entering the Genomic pages, be sure to select Rhesus Macaque as the species at the top left hand… Continue reading Genomic data in VDJbase
Human TRB AIRR-Seq datasets added
VDJbase now has a dataset based on TRB AIRR-Seq repertoires. This data is analysed in Omer et al., 2022, in which we demonstrate that methods developed for the inference of allelic variants in the B cell repertoire can also be applied to the T cell repertoire. Many T cell studies sequence just a short fraction… Continue reading Human TRB AIRR-Seq datasets added
Downloading data
Select the sample or allele data that you would like to download by using the filters, and press Download. For sample data, ‘csv’ will download a csv file with the information displayed on the Sample page, while ‘zip’ will download all files and reports for the selected samples. For alleles, ‘Gene information’ provides the information… Continue reading Downloading data