LongStitch: high-quality genome assembly correction and scaffolding using long reads.
LongStitch: high-quality genome assembly correction and scaffolding using long reads.
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DOI：
10.1186/s12859-021-04451-7
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发表时间：
2021-10-30
影响因子：
3
通讯作者：
Birol I
中科院分区：
文献类型：
--
作者：
Coombe L;Li JX;Lo T;Wong J;Nikolic V;Warren RL;Birol I
生成高质量的从头基因组组装是模型和非模型生物体基因组学研究的基础。近年来，长读长测序极大地有利于基因组组装和支架，这是一种通过使用长程信息对组装序列进行排序和定向的过程。与短读相比，长读能够更好地跨越重复的基因组区域，因此对于解决有问题的区域并帮助生成更完整的组装草案具有巨大的实用性。在这里，我们推出了 LongStitch，这是一个可扩展的管道，专门使用长读来校正和构建草图基因组组装。 LongStitch 结合了我们团队开发的多种工具，最多可运行三个阶段，其中包括初始组装校正（Tigmint-long），然后是两个增量脚手架阶段（ntLink 和 ARKS-long）。 Tigmint-long 和 ARKS-long 分别是错误组装校正和脚手架实用程序，之前为链接读取开发，我们对其进行了调整以适应长读取。在这里，我们描述了 LongStitch 管道并介绍了我们新的长读支架 ntLink，它利用轻量级最小化映射来连接重叠群。 LongStitch 使用相应的纳米孔长读长数据对秀丽隐杆线虫、水稻和三个不同人类个体的短读长和长读长组装体进行了测试，并将每个组装体的连续性从 1.2 倍提高到 304.6 倍（根据 NGA50 长度测量）。此外，在大多数测试中，与最先进的长读脚手架 LRScaf 相比，LongStitch 生成了更连续、更正确的组装，并且使用不到 23 GB 的 RAM 在不到 5 小时内持续改进了人类组装。由于其在使用长读长改进草图组装方面的有效性和效率，我们预计 LongStitch 将使各种从头基因组组装项目受益。 LongStitch 管道可在 https://github.com/bcgsc/longstitch 上免费获取。在线版本包含可在 10.1186/s12859-021-04451-7 获取的补充材料。
Generating high-quality de novo genome assemblies is foundational to the genomics study of model and non-model organisms. In recent years, long-read sequencing has greatly benefited genome assembly and scaffolding, a process by which assembled sequences are ordered and oriented through the use of long-range information. Long reads are better able to span repetitive genomic regions compared to short reads, and thus have tremendous utility for resolving problematic regions and helping generate more complete draft assemblies. Here, we present LongStitch, a scalable pipeline that corrects and scaffolds draft genome assemblies exclusively using long reads. LongStitch incorporates multiple tools developed by our group and runs in up to three stages, which includes initial assembly correction (Tigmint-long), followed by two incremental scaffolding stages (ntLink and ARKS-long). Tigmint-long and ARKS-long are misassembly correction and scaffolding utilities, respectively, previously developed for linked reads, that we adapted for long reads. Here, we describe the LongStitch pipeline and introduce our new long-read scaffolder, ntLink, which utilizes lightweight minimizer mappings to join contigs. LongStitch was tested on short and long-read assemblies of Caenorhabditis elegans, Oryza sativa, and three different human individuals using corresponding nanopore long-read data, and improves the contiguity of each assembly from 1.2-fold up to 304.6-fold (as measured by NGA50 length). Furthermore, LongStitch generates more contiguous and correct assemblies compared to state-of-the-art long-read scaffolder LRScaf in most tests, and consistently improves upon human assemblies in under five hours using less than 23 GB of RAM. Due to its effectiveness and efficiency in improving draft assemblies using long reads, we expect LongStitch to benefit a wide variety of de novo genome assembly projects. The LongStitch pipeline is freely available at https://github.com/bcgsc/longstitch. The online version contains supplementary material available at 10.1186/s12859-021-04451-7.
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影响因子：
9.2
作者：
Mendelowitz L;Pop M
通讯作者：
Pop M
影响因子：
7
作者：
Jackman, Shaun D.;Vandervalk, Benjamin P.;Birol, Inanc
通讯作者：
Birol, Inanc
影响因子：
4.4
作者：
Qin, Mao;Wu, Shigang;Ruan, Jue
通讯作者：
Ruan, Jue
DOI：
10.1038/s41576-020-0236-x
发表时间：
2020-10
期刊：
Nature reviews. Genetics
影响因子：
--
作者：
Logsdon GA;Vollger MR;Eichler EE
通讯作者：
Eichler EE
影响因子：
5.8
作者：
Li, Heng
通讯作者：
Li, Heng