检索结果-南通市图书馆

RGAAT: A Reference-based genome Assembly and Annotation Tool for New genomes and Upgrade of Known genomes

Genomics, Proteomics & Bioinformatics 2018年第5期16卷 373-381页

作者： Wanfei Liu Shuangyang Wu Qiang Lin Shenghan Gao Feng Ding Xiaowei Zhang Hasan Awad Aljohi Jun Yu Songnian Hu CAS Key Laboratory of genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China Joint Center for Genomics Research(JCGR) King Abdulaziz City for Science and Technology and Chinese Academy of SciencesRiyadh 11442Saudi Arabia University of Chinese Academy of Sciences Beijing 100049China Grail Scientific Co.Ltd. Shenyang 110000China Shenzhen Institute of Geriatrics Shenzhen 518020China

The rapid development of high-throughput sequencing technologies has led to a dramatic decrease in the money and time required for de novo genome sequencing or genome resequencing projects, with new genome sequences constantly released every week. Among such projects, the plethora of updated genome assemblies induces the requirement of versiondependent annotation files and other compatible public dataset for downstream analysis. To handlethese tasks in an efficient manner, we developed the reference-based genome assembly and annotation tool（RGAAT）, a flexible toolkit for resequencing-based consensus building and annotation update. RGAAT can detect sequence variants with comparable precision, specificity, and sensitivity to GATK and with higher precision and specificity than Freebayes and SAMtools on four DNAseq datasets tested in this study. RGAAT can also identify sequence variants based on cross-cultivar or cross-version genomic alignments. Unlike GATK and SAMtools/BCFtools, RGAAT builds the consensus sequence by taking into account the true allele frequency. Finally, RGAAT generates a coordinate conversion file between the reference and query genomes using sequence variants and supports annotation file transfer. Compared to the rapid annotation transfer tool（RATT）,RGAAT displays better performance characteristics for annotation transfer between different genome assemblies, strains, and species. In addition, RGAAT can be used for genome modification,genome comparison, and coordinate conversion. RGAAT is available at https://***/projects/rgaat/and https://***/wushyer/RGAAT;2 at no cost.

关键词： Variant identification genome assembly genome annotation genome comparison

来源：

维普期刊数据库

同方期刊数据库评论

在线全文

学校读者我要写书评

暂无评论

欢迎您,

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

在线全文

请选择保存的检索档案：

请选择收藏分类：

通借通还

欢迎您,

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

在线全文

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：