Sixth Researcher, Poznań, Poland.
Genomics and Experimental Evolution Group, Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland.
Methods Mol Biol. 2024;2809:37-66. doi: 10.1007/978-1-0716-3874-3_3.
AmpliSAS and AmpliHLA are tools for automatic genotyping of MHC genes from high-throughput sequencing data. AmpliSAS is designed specifically to analyze amplicon sequencing data from non-model species and it is able to perform de novo genotyping without any previous knowledge of the reference alleles. AmpliHLA is a human specific version; it performs HLA typing by comparing sequenced variants against human reference alleles from the IMGT/HLA database. Both tools are available in AmpliSAT web-server as well as scripts for local/server installation. Here we describe the installation and deployment of AmpliSAS and AmpliHLA Perl scripts and dependencies on a local or a server computer. We will show how to run them in the command line using as examples four genotyping protocols: the first two use amplicon sequencing data to genotype the MHC genes of a passerine bird and human respectively; the third and fourth present the HLA typing of a human cell line starting from RNA and exome sequencing data respectively.
AmpliSAS 和 AmpliHLA 是用于从高通量测序数据中自动进行 MHC 基因分型的工具。AmpliSAS 专门用于分析非模式物种的扩增子测序数据，并且能够在没有任何参考等位基因先验知识的情况下进行从头基因分型。AmpliHLA 是人类特有的版本；它通过将测序变体与来自 IMGT/HLA 数据库的人类参考等位基因进行比较来执行 HLA 分型。这两个工具都可在 AmpliSAT 网络服务器上使用，也可用于本地/服务器安装的脚本。在这里，我们将描述在本地或服务器计算机上安装和部署 AmpliSAS 和 AmpliHLA Perl 脚本以及依赖项的方法。我们将通过四个基因分型协议的示例展示如何在命令行中运行它们：前两个协议分别使用扩增子测序数据对雀形目鸟类和人类的 MHC 基因进行基因分型；第三和第四个协议分别介绍了从 RNA 和外显子测序数据开始的人类细胞系的 HLA 分型。
