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
MiAIRR metadata in VDJbase
VDJbase now provides AIRR-seq study metadata that follows the MiAIRR schema. For those studies that are listed in the iReceptor gateway, the metadata reflects that served by the gateway. For other studies, the metadata provided by VDJbase has been converted to MiAIRR attributes. This means that there are many more columns to choose from on… Continue reading MiAIRR metadata in VDJbase
Further updates to AIRR-seq IGH analysis
The IGH records are now processed with a pipeline that provides improved handling of sequences that are duplicated in the reference set: that is, multiple allele definitions having the same sequence. A bug in OGRDBstats that created incorrect full v-sequence alignments has also been fixed.
First Germline Sets Published on OGRDB
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
IGH Analysis updated
The analysis of the Human IGH dataset has now been updated to determine novel sequences based on the actual V length inferred by igblast, enabling greater recognition of variation at the 3′ end. To provide greater detail on the analysis, we now provide the commit id of the pipeline version used for analysis in the… Continue reading IGH Analysis updated
Introduction to OGRDB
Introduction to OGRDB In recent years it has become possible to sequence immune receptor repertoires (immunoglobulins and T cell receptors) at great depth. The accurate analysis of these repertoires requires a comprehensive understanding of the germline genes that give rise to the repertoire through V(D)J gene recombination. Even for well-studied species such as humans and… Continue reading Introduction to OGRDB
New inferred sequences accepted by IMGT
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.
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