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WiseScaffolder: an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data
Gregory K Farrant1,2, Mark Hoebeke3, Frédéric Partensky1,2
1Sorbonne Universités, UPMC Univ. Paris 06, UMR 7144, Station Biologique, CS 90074, 29688, Roscoff cedex, France.
WiseScaffolder, a new semi-automatic genome scaffolder, improves contiguity and aids manual refinement for prokaryotic and eukaryotic genomes. This tool enhances genome closure efficiency and quality.
Area of Science:
- Genomics
- Bioinformatics
Background:
- High-throughput sequencing enables de novo genome assembly, but closure often requires manual effort, leading to draft genomes.
- Existing automatic scaffolders improve genome quality but lack manual scaffolding efficiency.
Purpose of the Study:
- To introduce WiseScaffolder, a semi-automatic scaffolding tool that assists in chimera resolution and provides outputs for manual improvement.
- To evaluate WiseScaffolder's performance against other scaffolders using diverse datasets.
Main Methods:
- WiseScaffolder was tested on Synechococcus sp. WH8103, Rhodobacter sphaeroides, and Homo sapiens chromosome 14.
- Performance was compared to SSPACE, SOPRA, and SCARPA using contiguity statistics.
- A computer-assisted strategy for manual scaffolding improvement and genome finishing was developed.
Main Results:
- WiseScaffolder outperformed SSPACE, SOPRA, and SCARPA in contiguity statistics for all tested organisms.
- Scaffold reliability for WH8103 was validated via whole-genome alignment.
- The proposed strategy facilitated manual scaffolding improvement and genome circularization.
Conclusions:
- WiseScaffolder demonstrates superior efficiency compared to other scaffolders for both prokaryotic and eukaryotic genomes.
- The WiseScaffolder pipeline is valuable for genome projects aiming for complete genome sequences.
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