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

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Tools for working with germline sets

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. If you have issues using the germline sets… 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.

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

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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.

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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 IGH, IGK and IGL V-sequences for consideration. We hope to extend this to cover more species and loci soon. Qualification criteria… Continue reading Submitting inferences to OGRDB

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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

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