Abstract：
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.
摘要：
AmpliSAS和AmpliHLA是用于从高通量测序数据对MHC基因进行自动基因分型的工具。AmpliSAS专门设计用于分析来自非模型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的先前知识的情况下进行从头基因分型。AmpliHLA是人类特异性版本;它通过将测序的变体与来自IMGT/HLA数据库的人类参考等位基因进行比较来进行HLA分型。这两种工具均可在AmpliSATWeb服务器中使用，以及用于本地/服务器安装的脚本。在这里，我们描述了AmpliSAS和AmpliHLAPerl脚本的安装和部署以及在本地或服务器计算机上的依赖关系。我们将展示如何使用四种基因分型方案在命令行中运行它们：前两种使用扩增子测序数据分别对雀形目鸟和人的MHC基因进行基因型;第三和第四分别从RNA和外显子组测序数据开始呈现人细胞系的HLA分型。
