Department of Electrical and Computer Engineering, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece.
Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece.
BMC Bioinformatics. 2020 Sep 29;21(1):422. doi: 10.1186/s12859-020-03669-1.
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 .
抗原受体的特异性具有极高的多样性，这给计算和分析带来了重大挑战，尤其是在高通量免疫分析的下一代测序（NGS）时代。T 细胞受体/免疫球蛋白分析器（TRIP）工具提供了一种基于 IMGT/HighV-Quest 工具输出文件处理的深入分析机会，该工具是 NGS 免疫分析的标准工具，通过多个可互操作的模块。这些模块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）基因的使用、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（BcR IG）的克隆性，以及 BcR IG 基因中体细胞超突变的特征。TRIP 是一个在 R shiny 中实现的网络应用程序。
为了评估 TRIP 工具的效率和性能，进行了两项实验。第一项实验使用了一系列从 25 万到 100 万条序列的合成数据集，确定了工具的线性响应时间（大约 6 小时即可处理整个 BcR IG 数据管道中的 100 万条序列）。通过比较主要 TRIP 工作流程生成的结果与之前在 Galaxy 平台上使用的管道生成的结果，测试了工具的重现性。不出所料，两个工具之间没有明显差异；尽管 TRIP 管道中的预选过程似乎更为严格，但大约有 0.1%的重排被过滤掉，这对最终结果没有影响。
TRIP 是一个提供抗原受体基因序列数据分析服务的软件框架。它准确无误，包含数据整理、清理、分析和可视化功能，使用户能够构建适合其需求的管道。TRIP 可在 https://bio.tools/TRIP_-_T-cell_Receptor_Immunoglobulin_Profiler 上公开获取。
