Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly.
Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly.
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DOI：
10.1093/bioinformatics/btp377
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发表时间：
2009-11-01
期刊：
影响因子：
--
通讯作者：
Strous M
中科院分区：
文献类型：
--
作者：
Dutilh BE;Huynen MA;Strous M
动机：大多数微生物物种不能在实验室中培养。如果测序的群落是富集的并且测序覆盖率高，宏基因组测序仍然可以产生完整的基因组。然而，自然种群的复杂性可能导致富集培养物含有多种相关菌株。这种多样性可能会混淆现有的严格组装程序，并导致片段化组装，如果我们有相关的参考基因组可以用作支架，这是不必要的。结果如下：在这里，我们将来自菌株群体的短宏基因组测序读数映射到相关的参考基因组，并组成捕获群体序列一致性的基因组。我们表明，通过迭代的映射和组装过程，覆盖率增加，而与参考基因组的相似性降低。这表明组装体变得更少地依赖于参考基因组，并且接近多菌株群体的共有基因组。联系方式：dutilh@cmbi.ru.nl补充信息：补充数据可在生物信息学在线获得。
Motivation: Most microbial species can not be cultured in the laboratory. Metagenomic sequencing may still yield a complete genome if the sequenced community is enriched and the sequencing coverage is high. However, the complexity in a natural population may cause the enrichment culture to contain multiple related strains. This diversity can confound existing strict assembly programs and lead to a fragmented assembly, which is unnecessary if we have a related reference genome available that can function as a scaffold. Results: Here, we map short metagenomic sequencing reads from a population of strains to a related reference genome, and compose a genome that captures the consensus of the population's sequences. We show that by iteration of the mapping and assembly procedure, the coverage increases while the similarity with the reference genome decreases. This indicates that the assembly becomes less dependent on the reference genome and approaches the consensus genome of the multi-strain population. Contact: dutilh@cmbi.ru.nl Supplementary Information: Supplementary data are available at Bioinformatics online.
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影响因子：
56.9
作者：
Venter, JC;Remington, K;Smith, HO
通讯作者：
Smith, HO
来自非常短的读物的新型细菌基因组的基因促进组装。
影响因子：
4.3
作者：
Salzberg, Steven L.;Sommer, Daniel D.;Puiu, Daniela;Lee, Vincent T.
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通讯作者：
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影响因子：
5.1
作者：
Ettwig, Katharina F.;Shima, Seigo;Strous, Marc
通讯作者：
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