L_RNA_scaffolder: scaffolding genomes with transcripts

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.

Researchers at the Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences 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. They applied L_RNA_scaffolder to the highly polymorphic pearl oyster draft genome and the gene model length significantly increased.


Availability – L_RNA_scaffolder is available at http://www.fishbrowser.org/software/L_RNA_scaffolder.

  • Xue W, Li JT, Zhu YP, Hou GY, Kong XF, Kuang YY, Sun XW. (2013) L_RNA_scaffolder: scaffolding genomes with transcripts. BMC Genomics 14(1), 604. [abstract]
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