tigger

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TIgGER
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High-throughput sequencing of B cell immunoglobulin receptors is providing unprecedented insight into adaptive immunity. A key step in analyzing these data involves assignment of the germline V, D and J gene segment alleles that comprise each immunoglobulin sequence by matching them against a database of known V(D)J alleles. However, this process will fail for sequences that utilize previously undetected alleles, whose frequency in the population is unclear.

TIgGER is a computational method that significantly improves V(D)J allele assignments by first determining the complete set of gene segments carried by an individual (including novel alleles) from V(D)J-rearrange sequences. TIgGER can then infer a subject's genotype from these sequences, and use this genotype to correct the initial V(D)J allele assignments.

The application of TIgGER continues to identify a surprisingly high frequency of novel alleles in humans, highlighting the critical need for this approach. (TIgGER, however, can and has been used with data from other species.)

Core Abilities
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* Detecting novel alleles
* Inferring a subject's genotype
* Correcting preliminary allele calls

Required Input
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* A table of sequences from a single individual, with columns containing the following:
    * V(D)J-rearranged nucleotide sequence (in IMGT-gapped format)
    * Preliminary V allele calls
    * Preliminary J allele calls
    * Length of the junction region
* Germline Ig sequences in IMGT-gapped fasta format (e.g., as those downloaded from [IMGT/GENE-DB](https://www.imgt.org/genedb/)

The former can be created through the use of [IMGT/HighV-QUEST](https://www.imgt.org) and [Change-O](http://changeo.readthedocs.io).

Contact
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If you need help or have any questions, please contact the [Immcantation Group](mailto:immcantation@googlegroups.com).

If you have discovered a bug or have a feature request, you can open an issue using the [issue tracker](https://github.com/immcantation/tigger/issues).

To receive alerts about Immcantation releases, news, events, and tutorials, join the [Immcantation News](https://groups.google.com/g/immcantation-news) Google Group. [Membership settings](https://groups.google.com/g/immcantation-news/membership) can be adjusted to change the frequency of email updates.