L_RNA_scaffolder is a novel scaffolding tool using long trancriptome reads to scaffold genome fragments. The method is suitable for most genomes. The program could handle the transcript reads generated from 454/Sanger/Ion_Torrent sequencing, or de novo assembled with pair-end Illumina sequencing. Since the large introns cover most transcribed genome regions and RNA-sequencing is much less expensive than large insert library construction, the method provides a practical alternative to existing fosmid/BAC library_based approaches for scaffolding genome sequences in a cost effective way.If you feel that the software is useful, please cite Xue W, Li JT, Zhu YP, Hou GY, Kong XF, Kuang YY, Sun XW. L_RNA_scaffolder: scaffolding genomes with transcripts. BMC Genomics. 2013 Sep 8;14(1):604
News! We recently developed a novel scaffolder, named as 'PEP_scaffolder'. The method utilizes (homologous) proteins to scaffold contigs. It is much fast and has high accuracy. If you are interested, please go to PEP_scaffolder web site.