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Tools for processing immunosequencing data
Home Page: https://immunotools.github.io/immunotools/
License: Other
This project forked from immunotools/immunotools
Tools for processing immunosequencing data
Home Page: https://immunotools.github.io/immunotools/
License: Other
ImmunoTools package includes the following tools: - DiversityAnalyzer: a tool for basic processing immunosequencing (Rep-seq) data: V & J alignment, finding FRs / CDRs, and finding SHMs - IgEvolution: a tool for clonal analysis of antibody repertoires using immunosequencing data - IgScout: a tool for de novo inference of D (diversity genes) using Rep-seq data - Tandem CDR3 Finder: a tool for computing usage of D genes and finding CDR3s with tandem fusion of D-D genes Usage: ./diversity_analyzer.py -i rep_seq_library.fastq -o diversity_analyzer_output_dir -l LOCUS --org ORGANISM ./ig_evolution.py -i diversity_analyzer_output_dir -o igevolution_output_dir python igscout.py -i cdr3s.fasta -o igscout_output_dir -v V_genes.fasta -j J_genes.fasta python igscout_analyzer.py igscout_output_dir/inferred_segments.fasta known_D_genes.fasta output_annotation_dir python tandem_cdr3_finder.py IGHD.fa cdr3s.fasta tandem_finder_output_dir Installation instructions and manual can be found on the website: https://immunotools.github.io/immunotools/ Current contributors: Yana Safonova, Andrey Bzikadze, Vinnu Bhardwaj, Pavel A. Pevzner References: - Yana Safonova and Pavel A. Pevzner. IgEvolution: clonal analysis of antibody repertoires. bioRxiv 725424; doi: https://doi.org/10.1101/725424 - Yana Safonova and Pavel Pevzner. De novo inference of diversity genes and analysis of non-canonical V(DD)J recombination in immunoglobulins. Front. Immunol. | doi: 10.3389/fimmu.2019.00987
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