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增强重测序和变异检测能力

SMRT Analysis软件为序列比对、一致性序列检出、修正和变异检测提供了一套丰富的算法和程序。

适用于比对、一致性序列检出、修正和变异检测的SMRT Analysis算法

BLASR

Basic Local Alignment with Successive Refinement(BLASR)通过寻找序列和基因组之间评分最高的局部比对或组合,快速将序列映射到基因组。针对PacBio特别长的读取序列而优化,并利用丰富的质量值,BLASR能够快速而准确地映射序列。

Quiver

Quiver根据PacBio模板序列找到最相似的模板序列。利用条件随机域(CRF)方法对PacBio序列进行建模,这种方法在给定模板序列的情况下为序列分配概率。除了每条序列的碱基序列之外,Quiver还采用碱基检出QV值,以获得更准确的一致性序列检出。

LAA

Long Amplicon Analysis(长扩增子分析,LAA)从用PacBio SMRT技术测序的一组多倍体扩增子中找到定相的一致性序列。LAA有四个主要的分析步骤:粗略聚类、精细定相、一致性序列构建和后期处理。利用这种分析可处理多个分子的插入片段所产生的序列。

粗略聚类用于查找来自不同扩增子的读取序列组。来自每个粗略聚类的读取序列进入定相步骤,它利用基于Quiver的定相算法分离全长单体型。然后,使用Quiver算法对单体型进行修正,以获得高质量的一致性序列。最后,通过后期处理鉴定并去除假的一致性序列以及代表PCR假象的序列。

CCS

Circular Consensus Sequencing(CCS)算法计算由环化的单个DNA分子(即SMRTbell模板)(经滚环测序)所得的多重子读取序列(也称为“passes”)的一致性序列。 CCS用Quiver框架来获得特定passes数量下最佳的一致性结果。 使用这种算法可处理来自单个分子插入片段的序列,并估计上样到SMRT Cell中的插入片段的长度。

 

适用于比对、一致性序列检出、修正和变异检测的SMRT Analysis程序

BAM_Resequencing_Beta.1

该应用程序适用于全基因组或靶向重测序流程。分析程序筛取读取序列,并将其映射到所提供的参考序列。它利用Quiver鉴定一致性序列并检出变异。BAM_Resequencing_Beta.1在分析过程中使用BAM文件格式,明显比RS_resequencing更快。

RS_Resequencing

该应用程序适用于全基因组或靶向重测序流程。分析程序筛取读取序列,并将其与提供的参考序列进行比对。它利用Quiver鉴定一致性序列并检出变异。

RS_Minor Variant

此应用程序根据用户提供的参考序列检出杂合数据集中的少数变异。它特有定量检测的功能,足够灵敏到发现DNA样本中1%的基因组变异。

RS_Long_Amplicon_Analysis

此应用程序可确定混合扩增子数据中的定相一致性序列。它允许在大的基因组间隔中进行准确的等位基因定相和变异检出。LAA分析应用程序支持分析感兴趣的基因座中的新颖单体型,包括人类基因组中医学上很重要的HLA区域。它可以混合五个不同的扩增子。将序列聚类成高级别组,然后对每个组进行定相,并利用Quiver算法来检出一致性 序列。如果样本带有条形码标记,此分析工具则可以通过条形码来拆分读取序列。利用此分析工具可处理多个分子的插入片段的序列。

RS_ReadsOfInsert

此应用程序分析单个分子的序列。它生成每个分子的一致性序列,并估计在SMRT Cell上样的插入片段的长度。如果样本带有条形码标记,此分析工具则可以通过条形码来拆分序列。利用此分析可处理多个分子的插入片段的序列。

RS_ReadsOfInsert_Mapping

此应用程序生成单个分子的一致性序列。它筛取序列,将其映射到所提供的参考序列,并根据此参考序列鉴定一致性序列和单体型变异。

利用此分析方案可处理单个分子的插入片段的序列。

更多资源

  1. 深入了解BLASR
  2. 深入了解Quiver
  3. Quiver常见问题
  4. Variants.gff文件格式规范
  5. 少数变异和定相分析

 

若有意了解如何运用这种创新的软件来支持您的研究工作,请联系我们