Improved variation calling via an iterative backbone remapping and local assembly method for bacterial genomes.
Improved variation calling via an iterative backbone remapping and local assembly method for bacterial genomes.
复制标题
通过细菌基因组的迭代主干重映射和局部组装方法改进了变异识别。
DOI：
10.1016/j.ygeno.2012.07.015
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发表时间：
2012
期刊：
影响因子：
4.4
通讯作者：
Garner,HaroldR
中科院分区：
文献类型：
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作者：
Tae,Hongseok;Settlage,RobertE;Shallom,Shamira;Bavarva,JasminH;Preston,Dale;Hawkins,GregoryN;Adams,LGarry;Garner,HaroldR
测序数据分析仍然具有限制性和问题，特别是对于低复杂性重复序列和转座子元件，因为固有的测序错误和短序列读取长度。我们已经开发了一个程序，ReviSeq，它使用的混合方法组成的迭代重映射和本地组装后的细菌序列骨架。将该方法应用于6个猪布鲁氏菌现场分离株，并与新修订的B方法进行比较。与STAMPY/SAMtools、BWA/SAMtools、iCORN和BWA/PINDEL管道相比，suis 1330参考基因组平均每个样品多鉴定13、15、19和9个变体，并且平均每个样品分别排除4、2、3和19个变体。总之，使用这种迭代方法，当与参考相比时，我们平均鉴定了87种变体，包括SNV、短INDEL和长INDEL/菌株。我们的程序优于其他方法，特别是对于长INDEL调用。该程序可在http://reviseq.sourceforge.net上获得。
Sequencing data analysis remains limiting and problematic, especially for low complexity repeat sequences and transposon elements due to inherent sequencing errors and short sequence read lengths. We have developed a program, ReviSeq, which uses a hybrid method composed of iterative remapping and local assembly upon a bacterial sequence backbone. Application of this method to six Brucella suis field isolates compared to the newly revised B. suis 1330 reference genome identified on average 13, 15, 19 and 9 more variants per sample than STAMPY/SAMtools, BWA/SAMtools, iCORN and BWA/PINDEL pipelines, and excluded on average 4, 2, 3 and 19 variants per sample, respectively. In total, using this iterative approach, we identified on average 87 variants including SNVs, short INDELs and long INDELs per strain when compared to the reference. Our program outperforms other methods especially for long INDEL calling. The program is available at http://reviseq.sourceforge.net.