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SeqMule: automated pipeline for analysis of human exome/genome sequencing data

机译:SeqMule:用于分析人类外显子/基因组测序数据的自动化管道

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摘要

Next-generation sequencing (NGS) technology has greatly helped us identify disease-contributory variants for Mendelian diseases. However, users are often faced with issues such as software compatibility, complicated configuration, and no access to high-performance computing facility. Discrepancies exist among aligners and variant callers. We developed a computational pipeline, SeqMule, to perform automated variant calling from NGS data on human genomes and exomes. SeqMule integrates computational-cluster-free parallelization capability built on top of the variant callers, and facilitates normalization/intersection of variant calls to generate consensus set with high confidence. SeqMule integrates 5 alignment tools, 5 variant calling algorithms and accepts various combinations all by one-line command, therefore allowing highly flexible yet fully automated variant calling. In a modern machine (2 Intel Xeon X5650 CPUs, 48 GB memory), when fast turn-around is needed, SeqMule generates annotated VCF files in a day from a 30X whole-genome sequencing data set; when more accurate calling is needed, SeqMule generates consensus call set that improves over single callers, as measured by both Mendelian error rate and consistency. SeqMule supports Sun Grid Engine for parallel processing, offers turn-key solution for deployment on Amazon Web Services, allows quality check, Mendelian error check, consistency evaluation, HTML-based reports. SeqMule is available at http://seqmule.openbioinformatics.org.
机译:下一代测序(NGS)技术极大地帮助我们确定了孟德尔疾病的疾病归因变异体。但是,用户经常会遇到诸如软件兼容性,复杂的配置以及无法访问高性能计算工具等问题。 aligner和variant调用者之间存在差异。我们开发了一个计算管道SeqMule,以从人类基因组和外显子组的NGS数据执行自动变异调用。 SeqMule集成了基于变体调用程序的无计算群集并行化功能,并有助于变体调用的规范化/交集以高置信度生成共识集。 SeqMule集成了5种对齐工具,5种变体调用算法,并且可以通过单行命令接受各种组合,因此可以实现高度灵活但完全自动化的变体调用。在现代机器(2个Intel Xeon X5650 CPU,48 GB内存)中,当需要快速周转时,SeqMule每天可以从30倍的全基因组测序数据集中生成带注释的VCF文件。当需要更准确的呼叫时,SeqMule会生成共识呼叫集,与孟德尔错误率和一致性相比,该集合优于单个呼叫者。 SeqMule支持Sun Grid Engine进行并行处理,提供用于在Amazon Web Services上部署的交钥匙解决方案,允许质量检查,孟德尔错误检查,一致性评估,基于HTML的报告。 SeqMule可从http://seqmule.openbioinformatics.org获得。

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