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

ABSTRACT:

Background

Synthetic long reads (SLR) with long-range co-barcoding information are now widely applied in genomics research. Although several tools have been developed for each specific SLR technique, a robust standalone scaffolder with high efficiency is warranted for hybrid genome assembly.

Results

In this work, we developed a standalone scaffolding tool, SLR-superscaffolder, to link together contigs in draft assemblies using co-barcoding and paired-end read information. Our top-to-bottom scheme first builds a global scaffold graph based on Jaccard Similarity to determine the order and orientation of contigs, and then locally improves the scaffolds with the aid of paired-end information. We also exploited a screening algorithm to reduce the negative effect of misassembled c

SUBMITTER: Guo L 

PROVIDER: S-EPMC7993450 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature