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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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Versioning
No version available
Documentation
Maintainer
- person_outline Benny Chain
Additional information
Publications for Decombinator
Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine.
Decombinator citations
(7)High Throughput Sequencing of the Expressed Torafugu (Takifugu rubripes) Antibody Sequences Distinguishes IgM and IgT Repertoires and Reveals Evidence of Convergent Evolution
[…] ). 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
[…] 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
[…] 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
[…] 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 […]
Computational analysis of stochastic heterogeneity in PCR amplification efficiency revealed by single molecule barcoding
[…] 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
[…] 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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