Binnacle: Using Scaffolds to Improve the Contiguity and Quality of Metagenomic Bins.
Binnacle: Using Scaffolds to Improve the Contiguity and Quality of Metagenomic Bins.
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使用支架来提高宏基因组箱的连续性和质量。
DOI：
10.3389/fmicb.2021.638561
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发表时间：
2021
影响因子：
5.2
通讯作者：
Pop M
中科院分区：
文献类型：
--
作者：
Muralidharan HS;Shah N;Meisel JS;Pop M
高通量测序已经彻底改变了微生物学领域，然而，从整个宏基因组鸟枪测序数据重建生物体的完整基因组仍然是一个挑战。由于生物体丰度不均匀、基因组内和基因组间重复、测序错误和菌株水平变异，被分离的基因组通常高度碎片化。为了解决宏基因组组装的碎片化性质，科学家们依赖于一种称为分箱的过程，该过程将推断来自同一生物体的重叠群聚集在一起。现有的分箱算法使用样品内和样品间的寡核苷酸频率和重叠群丰度（覆盖度）将来自相同生物体的重叠群分组在一起。然而，这些算法经常错过短重叠群和来自具有不寻常覆盖或DNA组成特征的区域的重叠群，例如移动的元件。在这里，我们提出来自组装图的信息可以帮助当前的宏基因组分组策略。我们使用MetaCarvel，一个宏基因组支架工具，构建组装图，其中重叠群是节点，边缘是基于双端读段推断的。我们开发了一个工具，Binnacle，它从组装图中提取信息，并将支架聚类到综合箱中。Binnacle还提供包装器脚本来与现有的装箱方法集成。Binnacle管道可以在GitHub（https：//github.com/marbl/binnacle）上找到。我们表明，分箱基于图的支架，而不是重叠群，提高了所得箱的连续性和质量，并捕获了更广泛的一组被重建的生物体的基因。
High-throughput sequencing has revolutionized the field of microbiology, however, reconstructing complete genomes of organisms from whole metagenomic shotgun sequencing data remains a challenge. Recovered genomes are often highly fragmented, due to uneven abundances of organisms, repeats within and across genomes, sequencing errors, and strain-level variation. To address the fragmented nature of metagenomic assemblies, scientists rely on a process called binning, which clusters together contigs inferred to originate from the same organism. Existing binning algorithms use oligonucleotide frequencies and contig abundance (coverage) within and across samples to group together contigs from the same organism. However, these algorithms often miss short contigs and contigs from regions with unusual coverage or DNA composition characteristics, such as mobile elements. Here, we propose that information from assembly graphs can assist current strategies for metagenomic binning. We use MetaCarvel, a metagenomic scaffolding tool, to construct assembly graphs where contigs are nodes and edges are inferred based on paired-end reads. We developed a tool, Binnacle, that extracts information from the assembly graphs and clusters scaffolds into comprehensive bins. Binnacle also provides wrapper scripts to integrate with existing binning methods. The Binnacle pipeline can be found on GitHub (https://github.com/marbl/binnacle). We show that binning graph-based scaffolds, rather than contigs, improves the contiguity and quality of the resulting bins, and captures a broader set of the genes of the organisms being reconstructed.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
与痤疮相关的人皮肤微生物组中的痤疮丙酸杆菌菌株群体。
影响因子：
6.5
作者：
Fitz-Gibbon, Sorel;Tomida, Shuta;Chiu, Bor-Han;Lin Nguyen;Du, Christine;Liu, Minghsun;Elashoff, David;Erfe, Marie C.;Loncaric, Anya;Kim, Jenny;Modlin, Robert L.;Miller, Jeff F.;Sodergren, Erica;Craft, Noah;Weinstock, George M.;Li, Huiying
通讯作者：
Li, Huiying
DOI：
10.1093/bioinformatics/btq413
发表时间：
2010-09-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Guy L;Kultima JR;Andersson SG
通讯作者：
Andersson SG
影响因子：
14.9
作者：
Couvin D;Bernheim A;Toffano-Nioche C;Touchon M;Michalik J;Néron B;Rocha EPC;Vergnaud G;Gautheret D;Pourcel C
通讯作者：
Pourcel C
影响因子：
5.8
作者：
Li, Heng
通讯作者：
Li, Heng