Infers Novel Immunoglobulin Alleles from Sequencing Data
Example human immune repertoire data
Clean up nucleotide sequences
Find novel alleles from repertoire sequencing data
Determine which calls represent an unmutated allele
Generate evidence
Return the nucleotide sequences of a genotype
Find the location of mutations in a sequence
Determine the mutation counts from allele calls
Find mutation counts for frequency sequences
Infer a subject-specific genotype using a frequency method
Infer a subject-specific genotype using a Bayesian approach
Insert polymorphisms into a nucleotide sequence
Show a colorful representation of a genotype
Visualize evidence of novel V alleles
Read immunoglobulin sequences
Correct allele calls based on a personalized genotype
Select rows containing novel alleles
Sort allele names
Subsample repertoire
tigger: Infers Novel Immunoglobulin Alleles from Sequencing Data
tigger
Update IGHV allele names
Write to a fasta file
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. Citations: Gadala-Maria, et al (2015) <doi:10.1073/pnas.1417683112>, Gadala-Maria, et al (2019) <doi:10.3389/fimmu.2019.00129>.