High-throughput sequencing data from TCRs and Igs can provide valuable insights into the adaptive immune response, but bioinformatics pipelines for analysis of these data are constrained by the availability of accurate and comprehensive repositories of TCR and Ig alleles. We have created an analytical pipeline to recover immune receptor alleles from genome sequencing data. Applying this pipeline to data from the 1000 Genomes Project we have created Lym1K, a collection of immune receptor alleles that combines known, well-supported alleles with novel alleles found in the 1000 Genomes Project data. We show that Lym1K leads to a significant improvement in the alignment of short read sequences from immune receptors and that the addition of novel alleles discovered from genome sequence data are likely to be particularly significant for comprehensive analysis of populations that are not currently well represented in existing repositories of immune alleles.
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