amplimap：一款功能强大的工具，用于处理和分析靶向 NGS 数据。
amplimap: a versatile tool to process and analyze targeted NGS data.
机构信息
Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine.
Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
出版信息
Bioinformatics. 2019 Dec 15;35(24):5349-5350. doi: 10.1093/bioinformatics/btz582.
SUMMARY
amplimap is a command-line tool to automate the processing and analysis of data from targeted next-generation sequencing experiments with PCR-based amplicons or capture-based enrichment systems. From raw sequencing reads, amplimap generates output such as read alignments, annotated variant calls, target coverage statistics and variant allele counts and frequencies for each target base pair. In addition to its focus on user-friendliness and reproducibility, amplimap supports advanced features such as consensus base calling for read families based on unique molecular identifiers and filtering false positive variant calls caused by amplification of off-target loci.
AVAILABILITY AND IMPLEMENTATION
amplimap is available as a free Python package under the open-source Apache 2.0 License. Documentation, source code and installation instructions are available at https://github.com/koelling/amplimap.
摘要
amplimap 是一个命令行工具，用于自动化处理和分析基于 PCR 扩增子或捕获富集系统的靶向下一代测序实验的数据。从原始测序读取中，amplimap 生成输出，如读取比对、注释的变体调用、目标覆盖统计信息以及每个目标碱基对的变异等位基因计数和频率。除了注重用户友好性和可重复性外，amplimap 还支持高级功能，如基于独特分子标识符的读取家族的共识碱基调用，以及过滤由于靶标外位点扩增导致的假阳性变体调用。
可用性和实现
amplimap 是一个免费的 Python 包，在开源 Apache 2.0 许可证下可用。文档、源代码和安装说明可在 https://github.com/koelling/amplimap 上获得。
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