Host Subtraction, Filtering and Assembly Validations for Novel Viral Discovery Using Next Generation Sequencing Data.
Host Subtraction, Filtering and Assembly Validations for Novel Viral Discovery Using Next Generation Sequencing Data.
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DOI：
10.1371/journal.pone.0129059
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Heeney JL
中科院分区：
文献类型：
--
作者：
Daly GM;Leggett RM;Rowe W;Stubbs S;Wilkinson M;Ramirez-Gonzalez RH;Caccamo M;Bernal W;Heeney JL
使用下一代测序（NGS）从真核组织样本中鉴定新的病毒序列是具有挑战性的。问题可能包括病毒reads的低比例和拷贝数以及contigs（后组装）的高数量，这使得后续的病毒分析变得困难。使用短读映射工具、基于k-mer频率的滤波器和低复杂度滤波器，将装配算法与预装配宿主映射减法进行比较，已通过来自自然感染肝组织和模拟数据的Illumina数据验证了病毒发现的有效性。通过应用这些预装配滤波方法，装配组数显著减少（高达99.97%）。这种方法提供了一种有效的方法来最大化病毒组簇大小，并减少需要作为假定病毒核酸进行下游分析的组装组簇总数。
The use of next generation sequencing (NGS) to identify novel viral sequences from eukaryotic tissue samples is challenging. Issues can include the low proportion and copy number of viral reads and the high number of contigs (post-assembly), making subsequent viral analysis difficult. Comparison of assembly algorithms with pre-assembly host-mapping subtraction using a short-read mapping tool, a k-mer frequency based filter and a low complexity filter, has been validated for viral discovery with Illumina data derived from naturally infected liver tissue and simulated data. Assembled contig numbers were significantly reduced (up to 99.97%) by the application of these pre-assembly filtering methods. This approach provides a validated method for maximizing viral contig size as well as reducing the total number of assembled contigs that require down-stream analysis as putative viral nucleic acids.
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DOI：
10.1038/nrmicro2949
发表时间：
2013-02
期刊：
Nature reviews. Microbiology
影响因子：
--
作者：
通讯作者：
--
影响因子：
6.7
作者：
Grard G;Fair JN;Lee D;Slikas E;Steffen I;Muyembe JJ;Sittler T;Veeraraghavan N;Ruby JG;Wang C;Makuwa M;Mulembakani P;Tesh RB;Mazet J;Rimoin AW;Taylor T;Schneider BS;Simmons G;Delwart E;Wolfe ND;Chiu CY;Leroy EM
通讯作者：
Leroy EM
影响因子：
3.8
作者：
Boros, Akos;Nemes, Csaba;Reuter, Gabor
通讯作者：
Reuter, Gabor
影响因子：
3.7
作者：
Haiminen N;Kuhn DN;Parida L;Rigoutsos I
通讯作者：
Rigoutsos I
影响因子：
3.7
作者：
Daly GM;Bexfield N;Heaney J;Stubbs S;Mayer AP;Palser A;Kellam P;Drou N;Caccamo M;Tiley L;Alexander GJ;Bernal W;Heeney JL
通讯作者：
Heeney JL