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Decombinator specifications


Unique identifier OMICS_00001
Name Decombinator
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 3.1
Stability Stable
acora, biopython, regex, python-Levenshtein
Maintained Yes




No version available



  • person_outline Benny Chain

Additional information

Publications for Decombinator

Decombinator citations


High Throughput Sequencing of the Expressed Torafugu (Takifugu rubripes) Antibody Sequences Distinguishes IgM and IgT Repertoires and Reveals Evidence of Convergent Evolution

Front Immunol
PMCID: 5826340
PMID: 29515575
DOI: 10.3389/fimmu.2018.00251

[…] ). We counted the read number of each V, D, and J gene segment and calculated the frequency distribution. The computational strategy used for indel detection within the VDJ junctions was adapted from Decombinator (). […]


The T Cell Response to the Contact Sensitizer Paraphenylenediamine Is Characterized by a Polyclonal Diverse Repertoire of Antigen Specific Receptors

Front Immunol
PMCID: 5311069
PMID: 28261218
DOI: 10.3389/fimmu.2017.00162

[…] using version 2 chemistry 2x250PE kits.Sequences were first demultiplexed, according to the two indices that had been introduced into each sample, using a custom Python script. A modified version of Decombinator () was then used to identify the V and J region used, the number of nucleotide deletions from the V and the J gene, the inserted nucleotides, and the barcode information. Finally, a custo […]


Vidjil: A Web Platform for Analysis of High Throughput Repertoire Sequencing

PLoS One
PMCID: 5106020
PMID: 27835690
DOI: 10.1371/journal.pone.0166126

[…] nsertions.Many tools for the in-depth analysis of V(D)J recombinations were developed by IMGT [, ]. Recently, new software able to deal with up to millions of sequences have appeared: [], IgBlast [], Decombinator [], miTCR [], TCRKlass [], MiXCR [], IMSEQ []. At the heart of these programs is optimized comparison of the reads against germline databases to detect and quantify clonotypes, whose defi […]


High Throughput Sequencing Based Immune Repertoire Study during Infectious Disease

Front Immunol
PMCID: 5005336
PMID: 27630639
DOI: 10.3389/fimmu.2016.00336

[…] atabase ( (), despite the controversies about its validity (–). New V–D–J gene annotation tools based on various algorithms are reported, such as IgBLAST (), iHMMune-align (), and Decombinator (, ) (Table ). In addition, many integrated bioinformatic tools (MiTCR, LymAnalyzer, Change-O, etc.) for data processing are developed recently (–) (Table ), which provides various statis […]


Computational analysis of stochastic heterogeneity in PCR amplification efficiency revealed by single molecule barcoding

Sci Rep
PMCID: 4602216
PMID: 26459131
DOI: 10.1038/srep14629

[…] The FASTQ files produced on the MiSeq were demultiplexed based on the indices added through PCR and analysed using a modified version of Decombinator. Decombinator categorises each TCR sequence read by identifying its constituent V gene and J gene, along with the number of nucleotide deletions from each and the non-germline junctional […]


Tracking global changes induced in the CD4 T cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence

PMCID: 4221123
PMID: 25095879
DOI: 10.1093/bioinformatics/btu523

[…] variables, mitigates for sequencing error within V or J regions and determines the correct reading frame to extract the translated CDR3 region.The short length of the sequences made direct use of the Decombinator () problematic for unambiguous assignment of V and J gene segments, as the optimal unique tags that recognize the distinct V and J gene segments are located outside the sequenced window, […]


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Decombinator institution(s)
CoMPLEX Department, UCL, Gower Street, London, UK; Division of Infection and Immunity, The Cruciform Building, UCL, London, UK; Department of Immunology, Weizmann Institute of Science, Rehovot, Israel; Department of Computer Science, UCL, London, UK
Decombinator funding source(s)
Supported by the Engineering and Physical Sciences Research Council and the Medical Research Council, UK.

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