Profiling genes encoding the adaptive immune receptor repertoire with gAIRR Suite
Published in Frontiers in Immunology, 2022
gAIRR-Suite is a new toolkit profiling genes encoding the Adaptive Immune Receptor Repertoire (AIRR). We combined experimental and computational methods to genotype both documented and novel V, D, J genes in the human germline genome.
gAIRR-seq is a target sequencing method for T-cell receptor (TR) and Immunoglobulin (IG) V/J genes. We efficiently sequence more than 350x read coverage on the V/J genes. There are still around 250x coverage in the flanking sequence.
Based on target sequenced reads, gAIRR-call genotype both the documented and novel V/J genes. gAIRR-call can genotype all the TR and IG loci with decent accuracy.
In addition, we also provide gAIRR-annotate, an automated V/D/J genes annotation method for high-quality personal genomes such as T2T-CHM13.
The source code and AIRR annotations of GRCh37, GRCh38, and T2T-CHM13 are available at GitHub.
Recommended citation: Lin, Mao-Jan, et al. "Profiling genes encoding the adaptive immune receptor repertoire with gAIRR Suite." Frontiers in Immunology 13 (2022): 922513.
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