B-assembler: a circular bacterial genome assembler.
B-assembler: a circular bacterial genome assembler.
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B-assembler：循环细菌基因组组装器。
DOI：
10.1186/s12864-022-08577-7
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发表时间：
2022-05-11
期刊：
影响因子：
4.4
通讯作者：
中科院分区：
文献类型：
--
作者：
准确的细菌基因组从头组装是理解新细菌物种进化和发病机制的基础。第三代测序(TGS)的出现和流行使细菌基因组的组装以前所未有的速度进行。然而，目前大多数TGS基因组装器都是专门为人类或其他没有完整循环基因组的物种设计的。此外，由于许多细菌基因组中大量重复的DNA片段，再加上冗长的测序数据的高错误率，使得即使基因组大小相对较小，准确地组装它们的基因组仍然是非常具有挑战性的。因此，迫切需要开发一种优化的方法来解决这些问题。我们开发了B-汇编程序，它能够在只有长阅读数或短长阅读数的组合时组装细菌基因组。B-汇编程序利用了长读取的结构分辨率和短读取的准确性(如果适用)。它首先选择并校正超长的读数，以获得初始的重叠群。然后，它收集与初始重叠群末端重叠的读数。这种两轮组装程序加上优化的纠错，可以实现高置信度和循环的基因组组装。以几种细菌的合成和真实测序数据为基准，结果表明，长只读和混合读取模式都可以准确地组装环状细菌基因组，而不存在结构错误，并且与其他组装器相比，小错误更少。B-Assembly为细菌基因组组装提供了一种更好的解决方案，这将为下游的细菌基因组分析提供便利。网上版载有补充材料，可在10.1186/s12864-022-08577-7查阅。
Accurate bacteria genome de novo assembly is fundamental to understand the evolution and pathogenesis of new bacteria species. The advent and popularity of Third-Generation Sequencing (TGS) enables assembly of bacteria genomes at an unprecedented speed. However, most current TGS assemblers were specifically designed for human or other species that do not have a circular genome. Besides, the repetitive DNA fragments in many bacterial genomes plus the high error rate of long sequencing data make it still very challenging to accurately assemble their genomes even with a relatively small genome size. Therefore, there is an urgent need for the development of an optimized method to address these issues. We developed B-assembler, which is capable of assembling bacterial genomes when there are only long reads or a combination of short and long reads. B-assembler takes advantage of the structural resolving power of long reads and the accuracy of short reads if applicable. It first selects and corrects the ultra-long reads to get an initial contig. Then, it collects the reads overlapping with the ends of the initial contig. This two-round assembling procedure along with optimized error correction enables a high-confidence and circularized genome assembly. Benchmarked on both synthetic and real sequencing data of several species of bacterium, the results show that both long-read-only and hybrid-read modes can accurately assemble circular bacterial genomes free of structural errors and have fewer small errors compared to other assemblers. B-assembler provides a better solution to bacterial genome assembly, which will facilitate downstream bacterial genome analysis. The online version contains supplementary material available at 10.1186/s12864-022-08577-7.
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影响因子：
5.8
作者：
Li, Heng
通讯作者：
Li, Heng
影响因子：
14.9
作者：
Torresen, Ole K.;Star, Bastiaan;Linke, Dirk
通讯作者：
Linke, Dirk
DOI：
10.3390/antibiotics9120916
发表时间：
2020-12-16
期刊：
Antibiotics (Basel, Switzerland)
影响因子：
--
作者：
Fernández L;Cima-Cabal MD;Duarte AC;Rodriguez A;García P;García-Suárez MDM
通讯作者：
García-Suárez MDM
通过施用DNAASM的重复DNA区域的细菌基因组的从头组装。
影响因子：
3
作者：
Kuśmirek W;Nowak R
通讯作者：
Nowak R
DOI：
10.1016/j.cmi.2017.10.013
发表时间：
2018-04
期刊：
Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases
影响因子：
--
作者：
Besser J;Carleton HA;Gerner-Smidt P;Lindsey RL;Trees E
通讯作者：
Trees E