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 ()., 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 (, ). […]

[…] 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 […]

[…] (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 […]

[…] 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, […]

[…] (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 […]