Decombinator

[…] ). 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 (). […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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, […]