BACKGROUND Hi-C is derived from chromosome conformation capture (3C) and targets chromatin contacts on a genomic scale. This method has also been used frequently in scaffolding nucleotide sequences obtained by de novo genome sequencing and assembly, in which the number of resultant sequences rarely converges to the chromosome number. Despite its prevalent use, the sample preparation methods for Hi-C have not been intensively discussed, especially from the standpoint of genome scaffolding. RESULTS To gain insight into the best practice of Hi-C scaffolding, we performed a multifaceted methodological comparison using vertebrate samples and optimized various factors during sample preparation, sequencing, and computation. As a result, we identified several key factors that helped improve Hi-C scaffolding, including the choice and preparation of tissues, library preparation conditions, the choice of restriction enzyme(s), and the choice of scaffolding program and its usage. CONCLUSIONS This study provides the first comparison of multiple sample preparation kits/protocols and computational programs for Hi-C scaffolding by an academic third party. We introduce a customized protocol designated "inexpensive and controllable Hi-C (iconHi-C) protocol," which incorporates the optimal conditions identified in this study, and demonstrate this technique on chromosome-scale genome sequences of the Chinese softshell turtle Pelodiscus sinensis.

中文翻译：

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多方面的Hi-C基准测试：什么使染色体规模的基因组支架有所不同？

背景技术Hi-C源自染色体构象捕获（3C），并以基因组规模靶向染色质接触。该方法也经常用于从头进行基因组测序和组装获得的核苷酸序列的支架中，其中所得序列的数目很少会收敛到染色体数目。尽管已广泛使用Hi-C的样品制备方法，但从基因组支架的角度出发，尚未对其进行深入讨论。结果为了深入了解Hi-C脚手架的最佳实践，我们使用脊椎动物样品进行了多方面的方法比较，并在样品制备，测序和计算过程中优化了各种因素。结果，我们确定了有助于改善Hi-C脚手架的几个关键因素，包括组织的选择和制备，文库制备条件，限制酶的选择以及支架程序的选择及其用途。结论本研究首次提供了学术第三方对用于Hi-C支架的多种样品制备试剂盒/方案和计算程序的首次比较。我们引入定制的协议，称为“廉价且可控制的Hi-C（iconHi-C）协议”，该协议结合了本研究中确定的最佳条件，并在中华this中华绒螯蟹的染色体规模基因组序列上证明了该技术。结论本研究首次提供了学术第三方对用于Hi-C支架的多种样品制备试剂盒/方案和计算程序的首次比较。我们引入定制的协议，称为“廉价且可控制的Hi-C（iconHi-C）协议”，该协议结合了本研究中确定的最佳条件，并在中华this中华绒螯蟹的染色体规模基因组序列上证明了该技术。结论本研究首次提供了学术第三方对多种样品制备试剂盒/方案和Hi-C支架计算程序的比较。我们引入定制的协议，称为“廉价且可控制的Hi-C（iconHi-C）协议”，该协议结合了本研究中确定的最佳条件，并在中华this中华绒螯蟹的染色体规模基因组序列上证明了该技术。