There are many short-read aligners that can map short reads to a reference genome/sequence, and most of them can directly accept a FASTQ file as the input query file. However, the raw data usually need to be pre-processed. Few software programs specialize in pre-processing raw data generated by a variety of next-generation sequencing (NGS) technologies. Here, we present AUSPP, a Perl script-based pipeline for pre-processing and automatic mapping of NGS short reads. This pipeline encompasses quality control, adaptor trimming, collapsing of reads, structural RNA removal, length selection, read mapping, and normalized wiggle file creation. It facilitates the processing from raw data to genome mapping and is therefore a powerful tool for the steps before meta-analysis. Most importantly, since AUSPP has default processing pipeline settings for many types of NGS data, most of the time, users will simply need to provide the raw data and genome. AUSPP is portable and easy to install, and the source codes are freely available at https://github.com/highlei/AUSPP .

中文翻译：

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AUSPP：通用短读预处理包

有许多短读比对器可以将短读比对到参考基因组/序列，其中大多数可以直接接受 FASTQ 文件作为输入查询文件。但是，原始数据通常需要进行预处理。很少有软件程序专门用于预处理由各种下一代测序 (NGS) 技术生成的原始数据。在这里，我们介绍了 AUSPP，这是一个基于 Perl 脚本的管道，用于 NGS 短读段的预处理和自动映射。该管道包括质量控制、适配器修剪、读取折叠、结构 RNA 去除、长度选择、读取映射和标准化摆动文件创建。它促进了从原始数据到基因组作图的处理，因此是元分析之前步骤的有力工具。最重要的是，由于 AUSPP 对许多类型的 NGS 数据都有默认的处理流程设置，因此大多数情况下，用户只需提供原始数据和基因组即可。AUSPP 可移植且易于安装，源代码可在 https://github.com/highlei/AUSPP 免费获得。