MutAid: Sanger and NGS Based Integrated Pipeline for Mutation Identification, Validation and Annotation in Human Molecular Genetics

Traditional Sanger sequencing as well as Next-Generation Sequencing have been used for the identification of disease causing mutations in human molecular research. The majority of currently available tools are developed for research and explorative purposes and often do not provide a complete, efficient, one-stop solution. As the focus of currently developed tools is mainly on NGS data analysis, no integrative solution for the analysis of Sanger data is provided and consequently a one-stop solution to analyze reads from both sequencing platforms is not available. We have therefore developed a new pipeline called MutAid to analyze and interpret raw sequencing data produced by Sanger or several NGS sequencing platforms. It performs format conversion, base calling, quality trimming, filtering, read mapping, variant calling, variant annotation and analysis of Sanger and NGS data under a single platform. It is capable of analyzing reads from multiple patients in a single run to create a list of potential disease causing base substitutions as well as insertions and deletions. MutAid has been developed for expert and non-expert users and supports four sequencing platforms including Sanger, Illumina, 454 and Ion Torrent. Furthermore, for NGS data analysis, five read mappers including BWA, TMAP, Bowtie, Bowtie2 and GSNAP and four variant callers including GATK-HaplotypeCaller, SAMTOOLS, Freebayes and VarScan2 pipelines are supported. MutAid is freely available at https://sourceforge.net/projects/mutaid.

传统桑格测序（Sanger sequencing）以及下一代测序（Next-Generation Sequencing，NGS）已广泛应用于人类分子研究领域的致病突变鉴定工作。当前多数已发布的工具均为研究探索需求开发，往往无法提供完整、高效的一站式分析解决方案。由于当前主流开发工具的核心聚焦点多为NGS数据分析，并未针对桑格测序数据提供整合分析方案，因此目前尚无能够同时处理两类测序平台原始读段的一站式分析流程。为此，我们开发了一款名为MutAid的全新分析流程，用于分析并解读桑格测序或多款下一代测序平台产生的原始测序数据。该流程可在单一平台内完成桑格与NGS数据的格式转换、碱基识别、质量修剪、过滤、读段比对、变异检测、变异注释及后续分析工作。其支持单次运行中对多名患者的测序读段进行分析，进而生成潜在致病碱基替换、插入与缺失的变异列表。MutAid面向专业与非专业用户开发，支持包括桑格测序、Illumina、454及Ion Torrent在内的四款测序平台。此外，针对NGS数据分析场景，其支持BWA、TMAP、Bowtie、Bowtie2与GSNAP共五款读段比对工具，以及GATK-HaplotypeCaller、SAMTOOLS、Freebayes与VarScan2共四款变异检测流程。MutAid可通过https://sourceforge.net/projects/mutaid免费获取。