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

Abstract

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.