Abstract
While aiming to determine orientations and orders of fragmented contigs, scaffolding is an essential step of assembly pipelines and can make assembly results more complete. Most existing scaffolding tools adopt the scaffold graph approach. However, constructing an accurate scaffold graph is still a challenge task. Removing potential false relationships is a key to achieve a better scaffolding performance, while most scaffolding approaches neglect the impacts of uneven sequencing depth that may cause more sequencing errors, and finally result in many false relationships. In this paper, we present a new scaffolding method LSLS (Loose-Strict-Loose Scaffolding), which is based on path extension. LSLS uses different strategies to extend paths, which can be more adaptive to different sequencing depths. For the problem of multiple paths, we designed a score function, which is based on the distribution of read pairs, to evaluate the reliability of path candidates and extend them with the paths which have the highest score. Besides, LSLS contains a new gap estimation method, which can estimate gap sizes more precisely. The experiment results on the two standard datasets show that LSLS can get better performance.
Published Version
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
