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SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme

By Lidong Guo, Mengyang Xu, Wenchao Wang, Shengqiang Gu, Xia Zhao, Fang Chen, Ou Wang, Xun Xu, Guangyi Fan, Li Deng, Xin Liu

Posted 08 Sep 2019
bioRxiv DOI: 10.1101/762385

Synthetic long reads (SLR) with long-range co-barcoding information have been recently developed and widely applied in genomics researches. We proposed a scaffolding model of the co-barcoding information and developed a scaffolding tool with adopting a top-to-bottom scheme to make full use of the complementary information in SLR datasets and a screening algorithm to reduce negative effects from misassembled contigs in an input assembly. In comparison with other available SLR scaffolding tools, our tool obtained the best quality improvement for different input assemblies, especially for those assembled by the next-generation sequencing reads, where the improvement of contiguity is about several hundred-folds. ### Competing Interest Statement The authors have declared no competing interest. * SLR : Synthetic long reads stLFR : Single tube long fragment reads NGS : next generation sequencing LDF : long DNA fragment CPT-seq : contiguity preserving transposition sequencing MST : minimum spanning tree PE : paired-end 10XG-linked reads : 10X Genomics Chromium technology SMRT : single molecular real time sequencing HG001 : the human whole genome for cell line NA12878 JS : Jaccard Similarity NB : number of shared barcodes Chr19 : hromosome 19.

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