Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing.
Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing.
复制标题
DOI：
10.1186/1471-2105-11-572
复制
发表时间：
2010-11-23
影响因子：
3
通讯作者：
Milosavljevic A
中科院分区：
文献类型：
--
作者：
Coarfa C;Yu F;Miller CA;Chen Z;Harris RA;Milosavljevic A
表观基因组分析的大规模并行测序读数使基因组和表观基因组变异的综合分析成为可能。PASH 3.0执行序列比较和读取映射，可作为各种可配置分析管道中的模块使用，包括通过全基因组亚硫酸氢盐测序进行芯片-序列和甲基组映射。PASH 3.0的精确度和速度与利基程序相当，可快速绘制短读数图，并在新一代大规模并行测序技术生成的较长读数上超过它们的性能。通过利用更长的读取长度，Pash 3.0将读取映射到包含重复元件和多态位点(包括Indel多态)的基因组DNA的大部分上。我们基于公开的全基因组鸟枪亚硫酸盐测序数据，通过分析CpG甲基化、CpG SNPs和印记之间的相互作用，证明了Pash 3.0的多功能性。PASH 3.0使用了缺口k-mer比对，这是一种非基于种子的比较方法，它是使用多位置哈希表实现的。这使得Pash 3.0可以在不同的硬件平台上运行，包括具有标准RAM容量的单个计算机、多核硬件架构和大型集群。
Massively parallel sequencing readouts of epigenomic assays are enabling integrative genome-wide analyses of genomic and epigenomic variation. Pash 3.0 performs sequence comparison and read mapping and can be employed as a module within diverse configurable analysis pipelines, including ChIP-Seq and methylome mapping by whole-genome bisulfite sequencing. Pash 3.0 generally matches the accuracy and speed of niche programs for fast mapping of short reads, and exceeds their performance on longer reads generated by a new generation of massively parallel sequencing technologies. By exploiting longer read lengths, Pash 3.0 maps reads onto the large fraction of genomic DNA that contains repetitive elements and polymorphic sites, including indel polymorphisms. We demonstrate the versatility of Pash 3.0 by analyzing the interaction between CpG methylation, CpG SNPs, and imprinting based on publicly available whole-genome shotgun bisulfite sequencing data. Pash 3.0 makes use of gapped k-mer alignment, a non-seed based comparison method, which is implemented using multi-positional hash tables. This allows Pash 3.0 to run on diverse hardware platforms, including individual computers with standard RAM capacity, multi-core hardware architectures and large clusters.
登录
查看更多内容
影响因子：
9.8
作者：
Schalkwyk, Leonard C.;Meaburn, Emma L.;Mill, Jonathan
通讯作者：
Mill, Jonathan
影响因子：
30.8
作者：
Iafrate, AJ;Feuk, L;Lee, C
通讯作者：
Lee, C
影响因子：
3
作者：
Smith AD;Xuan Z;Zhang MQ
通讯作者：
Zhang MQ
影响因子：
46.9
作者：
通讯作者：
--
影响因子：
64.8
作者：
通讯作者：
--