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

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Documentation


Maintainer


  • person_outline Benny Chain <>

Additional information


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

Publications for Decombinator

Decombinator in publications

 (9)
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 ()., capture–recapture analysis was performed to assess the cdr-h3 diversity. cdr-h3 aa sequences were clustered into lineages according to sequence similarity using cd-hit (, ). […]

PMCID: 5643411
PMID: 29075258
DOI: 10.3389/fimmu.2017.01267

[…] in figure . a detailed description of each step is outlined below:, the analysis of the fastq files is carried out using a suite of python scripts available at https://github.com/innate2adaptive/decombinator. the repository also contains help files and test data. the core tcr assignment is based on a modified version of the original decombinator software (), which uses a tag-based […]

PMCID: 5390035
PMID: 28450864
DOI: 10.3389/fimmu.2017.00430

[…] (days 60 experiment 1); and two runs with three ova + cfa and two cfa alone on each run (days 7 and 60)., raw sequence data were analyzed and error corrected using a short read modification of decombinator as described in detail previously (). the fastq files are available at http://www.ncbi.nlm.nih.gov/sra/?term=srp075893., in order to compare two cdr3β amino acid sequences, two measures […]

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

[…] 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, […]

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

[…] (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 […]


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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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