title: L_RNA_scaffolder: scaffolding genomes with transcripts.
abstract: 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.
authors.affiliation: The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China. lijt83@gmail.com.
authors.forename: Wei
authors.initials: W
authors.lastname: Xue
authors.forename: Jiong-Tang
authors.initials: JT
authors.lastname: Li
authors.forename: Ya-Ping
authors.initials: YP
authors.lastname: Zhu
authors.forename: Guang-Yuan
authors.initials: GY
authors.lastname: Hou
authors.forename: Xiang-Fei
authors.initials: XF
authors.lastname: Kong
authors.forename: You-Yi
authors.initials: YY
authors.lastname: Kuang
authors.forename: Xiao-Wen
authors.initials: XW
authors.lastname: Sun
mesh_terms: D000818:Animals; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006801:Humans; D049911:Pinctada / Q000235:genetics; D012313:RNA / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D059467:Transcriptome; D015027:Zebrafish / Q000235:genetics
chemical_list: D012313:RNA