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L_RNA_scaffolder: scaffolding genomes with transcripts

文献类型： 外文期刊

作者： Xue, Wei 1 ; Li, Jiong-Tang 1 ; Zhu, Ya-Ping 1 ; Hou, Guang-Yuan 1 ; Kong, Xiang-Fei 1 ; Kuang, You-Yi 4 ; Sun, Xiao-W 1 ;

作者机构： 1.Chinese Acad Fishery Sci, Ctr Appl Aquat Genom, Beijing 100141, Peoples R China

2.Shanghai Ocean Univ, Coll Fisheries & Life Sci, Shanghai 201306, Peoples R China

3.Chinese Acad Sci, Key Lab Computat Biol, CAS MPG Partner Inst Computat Biol, Shanghai Inst Biol Sci, Shanghai 200031, Peoples R China

4.Chinese Acad Fishery Sci, Heilongjiang River Fisheries Res Inst, Harbin 150001, Peoples R China

关键词： L_RNA_scaffolder;Scaffolding;Transcriptome;Genome

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2013 年 14 卷

页码：

收录情况： SCI

摘要： Background: Generation of large mate-pair libraries is necessary for de novo genome assembly but the procedure is complex and time-consuming. Furthermore, in some complex genomes, it is hard to increase the N50 length even with large mate-pair libraries, which leads to low transcript coverage. Thus, it is necessary to develop other simple scaffolding approaches, to at least solve the elongation of transcribed fragments. Results: We describe L_RNA_scaffolder, a novel genome scaffolding method that uses long transcriptome reads to order, orient and combine genomic fragments into larger sequences. To demonstrate the accuracy of the method, the zebrafish genome was scaffolded. With expanded human transcriptome data, the N50 of human genome was doubled and L_RNA_scaffolder out-performed most scaffolding results by existing scaffolders which employ mate-pair libraries. In these two examples, the transcript coverage was almost complete, especially for long transcripts. We applied L_RNA_scaffolder to the highly polymorphic pearl oyster draft genome and the gene model length significantly increased. Conclusions: The simplicity and high-throughput of RNA-seq data makes this approach suitable for genome scaffolding. L_RNA_scaffolder is available at http://www.fishbrowser.org/software/L_RNA_scaffolder.

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