Antigen receptors are characterized by an extreme diversity of specificities, which poses major computational and analytical challenges, particularly in the era of high-throughput immunoprofiling by next generation sequencing (NGS). The T cell Receptor/Immunoglobulin Profiler (TRIP) tool offers the opportunity for an in-depth analysis based on the processing of the output files of the IMGT/HighV-Quest tool, a standard in NGS immunoprofiling, through a number of interoperable modules. These provide detailed information about antigen receptor gene rearrangements, including variable (V), diversity (D) and joining (J) gene usage, CDR3 amino acid and nucleotide composition and clonality of both T cell receptors (TR) and B cell receptor immunoglobulins (BcR IG), and characteristics of the somatic hypermutation within the BcR IG genes. TRIP is a web application implemented in R shiny. Two sets of experiments have been performed in order to evaluate the efficiency and performance of the TRIP tool. The first used a number of synthetic datasets, ranging from 250k to 1M sequences, and established the linear response time of the tool (about 6 h for 1M sequences processed through the entire BcR IG data pipeline). The reproducibility of the tool was tested comparing the results produced by the main TRIP workflow with the results from a previous pipeline used on the Galaxy platform. As expected, no significant differences were noted between the two tools; although the preselection process seems to be stricter within the TRIP pipeline, about 0.1% more rearrangements were filtered out, with no impact on the final results. TRIP is a software framework that provides analytical services on antigen receptor gene sequence data. It is accurate and contains functions for data wrangling, cleaning, analysis and visualization, enabling the user to build a pipeline tailored to their needs. TRIP is publicly available at https://bio.tools/TRIP_-_T-cell_Receptor_Immunoglobulin_Profiler .

中文翻译：

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TRIP-T细胞受体/免疫球蛋白分析仪

抗原受体的特征是具有极大的特异性多样性，这带来了重大的计算和分析挑战，特别是在通过下一代测序（NGS）进行高通量免疫分析的时代。T细胞受体/免疫球蛋白分析仪（TRIP）工具通过多个可互操作的模块，基于对IMGS / HighV-Quest工具（NGS免疫分析的标准）的输出文件的处理，提供了进行深入分析的机会。这些提供了有关抗原受体基因重排的详细信息，包括可变（V），多样性（D）和连接（J）基因用法，CDR3氨基酸和核苷酸组成以及T细胞受体（TR）和B细胞受体免疫球蛋白的克隆性（ BcR IG），以及BcR IG基因内体细胞超突变的特征。TRIP是用R Shiny实现的Web应用程序。为了评估TRIP工具的效率和性能，已经进行了两组实验。第一个使用了许多合成数据集，范围从250k到1M序列，并建立了工具的线性响应时间（对于通过整个BcR IG数据管道处理的1M序列大约需要6小时）。测试了该工具的可重复性，将TRIP主工作流程产生的结果与Galaxy平台上使用的先前管道的结果进行了比较。不出所料，这两个工具之间没有发现显着差异。尽管TRIP管道中的预选过程似乎更加严格，但过滤掉了约0.1％的重排，对最终结果没有影响。TRIP是一个软件框架，可提供有关抗原受体基因序列数据的分析服务。它是准确的，并且包含用于数据整理，清理，分析和可视化的功能，使用户能够建立适合其需求的管道。TRIP可从https://bio.tools/TRIP_-_T-cell_Receptor_Immunoglobulin_Profiler公开获得。