Immunotools
- Diversity Analyzer is a tool for annotation and diversity analysis of full-length adaptive immune repertoires (antibodies or TCRs).
- IgEvolution, a tool for clonal analysis of antibody repertoires using immunosequencing data.
- IgScout, a tool for de novo inference of immunoglobulin D genes and finding CDR3s with tandem fusion of D-D genes
Installation instructions are described in the manual.
Diversity Analyzer
Diversity Analyzer takes full-length sequences of adaptive immune receptors as an input. Tool expects that input sequences cover entire variable regions of antibody or TCR: from the start of V segment to the end of J segment. Tool is able to process raw Rep-seq libraries, as well as constructed repertoires.
To launch DiversityAnalyzer, type:
./diversity_analyzer.py -i INPUT_FILE -o DIVERSITY_ANALYZER_DIR -l LOCUS
- INPUT_FILE: input sequences of adaptive immune receptors in FASTA/FASTQ format;
- DIVERSITY_ANALYZER_DIR: output directory of Diversity Analyzer. Please note that DiversityAnalyzer checks the existence of DIVERSITY_ANALYZER_DIR, removes it if it exists, and creates an empty directory with name DIVERSITY_ANALYZER_DIR. So, we recommend not to specify an existing directory (e.g., the home directory) as DIVERSITY_ANALYZER_DIR!
- LOCUS: name of IG / TR locus that will be used for alignment. Possible values: ALL / IG / IGH / IGK / IGL / TR / TRA / TRB / TRG / TRD.
For further details, please visit Diversity Analyzer page.
IgEvolution
IgEvolution performs simultaneous repertoire and clonal tree reconstruction of a Rep-seq library taken from an antibody repertoire. To run IgEvolution, first run DiversityAnalyzer and then provide the resulting output directory as an input:
./ig_evolution.py -i DIVERSITY_ANALYZER_DIR -o IGEVOLUTION_DIR
- DIVERSITY_ANALYZER_DIR: output directory of Diversity Analyzer. IgEvolution uses the results of VJ and CDR labeling of a Rep-seq library.
- IGEVOLUTION_DIR: output directory of IgEvolution.
For further details, please visit IgEvolution page.
IgScout
IgScout performs de novo inference of immunoglobulin D (diversity genes) using Rep-seq data, computes usage of D genes, and identifies CDR3s with tandem fusion of D-D genes. IgScout takes CDR3 sequences in FASTA format as an input and reports candidates for inferred D genes:
python igscout.py -i cdr3s.fasta -o IGSCOUT_OUTPUT_DIR
For further details, please look at the manual.
Citation and feedback
- If you use DiversityAnalyzer in your research, please cite: Shlemov A, Bankevich S, Bzikadze A, Turchaninova MA, Safonova Y, Pevzner PA. Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads. J Immunol. 2017 Nov 1;199(9):3369-3380.
- If you use IgEvolution, please cite: Yana Safonova and Pavel A. Pevzner. IgEvolution: clonal analysis of antibody repertoires. bioRxiv 725424; doi: https://doi.org/10.1101/725424.
- If you use IgScout, please cite: Yana Safonova and Pavel A. Pevzner. De novo inference of diversity genes and analysis of non-canonical V(DD)J recombination in immunoglobulins. Front Immunol. 2019. 10:987.
If you have any questions or troubles with running ImmunoTools, please contact Yana Safonova. We also will be happy to hear your suggestions about improvement of our tools!