Reducing assembly complexity of microbial genomes with single-molecule sequencing.
Reducing assembly complexity of microbial genomes with single-molecule sequencing.
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DOI：
10.1186/gb-2013-14-9-r101
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发表时间：
2013
期刊：
影响因子：
12.3
通讯作者：
Phillippy AM
中科院分区：
文献类型：
--
作者：
Koren S;Harhay GP;Smith TP;Bono JL;Harhay DM;Mcvey SD;Radune D;Bergman NH;Phillippy AM
第一代和第二代DNA测序仪器输出的短读段不能完全重建微生物染色体。因此，大多数基因组都没有完成，因为需要大量的资源来手动填补草案汇编中的空白。第三代单分子测序通过大大增加测序读段长度来解决这个问题，这简化了组装问题。为了衡量单分子测序对微生物基因组组装的好处，我们对6种细菌的基因组进行了测序和组装，并分析了2，267种完整细菌和古细菌的重复复杂性。我们的研究结果表明，大多数已知的细菌和古细菌基因组可以组装没有差距，在成品级的质量，使用一个单一的PacBio RS测序库。这些单文库组装也比典型的短读段组装和短读段和长读段的混合组装更准确。长的单分子测序数据的自动组装将大多数基因组的微生物整理成本降低到1,000美元，预计该技术的未来进展将降低成本。预计这将增加已完成的基因组数量，提高微生物基因组数据库的质量，并实现对泛基因组和染色体组织的高保真、人群规模的研究。
The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required to manually close gaps in draft assemblies. Third-generation, single-molecule sequencing addresses this problem by greatly increasing sequencing read length, which simplifies the assembly problem. To measure the benefit of single-molecule sequencing on microbial genome assembly, we sequenced and assembled the genomes of six bacteria and analyzed the repeat complexity of 2,267 complete bacteria and archaea. Our results indicate that the majority of known bacterial and archaeal genomes can be assembled without gaps, at finished-grade quality, using a single PacBio RS sequencing library. These single-library assemblies are also more accurate than typical short-read assemblies and hybrid assemblies of short and long reads. Automated assembly of long, single-molecule sequencing data reduces the cost of microbial finishing to $1,000 for most genomes, and future advances in this technology are expected to drive the cost lower. This is expected to increase the number of completed genomes, improve the quality of microbial genome databases, and enable high-fidelity, population-scale studies of pan-genomes and chromosomal organization.
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DOI：
10.1093/bioinformatics/bts330
发表时间：
2012-08-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
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