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Decombinator specifications

Information


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
Requirements
acora, biopython, regex, python-Levenshtein
Maintained Yes

Download


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Versioning


No version available

Documentation


Maintainer


  • person_outline Benny Chain

Additional information


https://innate2adaptive.github.io/Decombinator/

Publications for Decombinator

Decombinator citations

 (7)
library_books

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

2018
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 (). […]

library_books

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

2017
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 […]

library_books

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

2016
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 […]

library_books

High Throughput Sequencing Based Immune Repertoire Study during Infectious Disease

2016
Front Immunol
PMCID: 5005336
PMID: 27630639
DOI: 10.3389/fimmu.2016.00336

[…] atabase (http://www.imgt.org) (), 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 […]

library_books

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

2015
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 […]

library_books

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

2014
Bioinformatics
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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