Infers the V genotype of an individual from immunoglobulin (Ig)
repertoire sequencing data (AIRR-Seq, Rep-Seq). Includes detection of
any novel alleles. This information is then used to correct existing V
allele calls from among the sample sequences.
Gadala-Maria, et al (2015)
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.)
generateEvidencethat was reporting amino acids mutations as NA instead of gaps.
reassignAllelesoccuring with single match genotypes.
selectNovelimproperly removing all identical novel alleles, rather than keeping a single entry.
genotypeFastawill now retain IMGT-numbering spacers as
.characters instead of converting them to
findNovelAllelescausing overly aggressive minimum sequence threshold filtering.
generateEvidenceto build a complete evidence table from the results of
findNovelAllelesand adjusted the definitions/names of some existing columns.
reassignAllelesto provide options for maintaining reassignments at the gene (previous
TRUEbehavior), family, or repertoire level.
Backwards Incompatible Refactors:
inferGenotypewas alter for clarity.
reassignAllelesso that it returns the input data.frame with the
V_CALL_GENOTYPEDcolumn appended or overwritten.
cleanSeqswill no longer replace
inferGenotypewould break when performing check for alleles that could not be distinguished.
inferGenotypewould break if all sequences submitted were from a single gene and
find_unmutatedwas set to
findNovelAlleles()was not running in parallel, even when