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Multi-CSAR: a multiple reference-based contig scaffolder using algebraic rearrangements.

Kun-Tze Chen1, Hsin-Ting Shen1, Chin Lung Lu2

  • 1Department of Computer Science, National Tsing Hua University, Hsinchu, 30013, Taiwan.

BMC Systems Biology
|January 2, 2019
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Summary
This summary is machine-generated.

Scaffolding genomes using multiple references improves accuracy. Multi-CSAR, a new tool, accurately orders and orients draft genome contigs using multiple genomes, outperforming existing methods.

Keywords:
BioinformaticsContigMultiple reference genomesScaffoldingSequencing

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Genome assembly from short reads involves scaffolding to order and orient contigs.
  • Existing scaffolding tools rely on single reference genomes, which can be insufficient for distant or rearranged genomes.
  • There is a need for scaffolding tools that leverage multiple reference genomes.

Purpose of the Study:

  • To develop a novel scaffolding tool, Multi-CSAR, that utilizes multiple reference genomes.
  • To improve the accuracy and efficiency of genome scaffolding.

Main Methods:

  • A heuristic method was employed to develop the Multi-CSAR scaffolder.
  • Multi-CSAR uses multiple, potentially incomplete, reference genomes to scaffold a target draft genome.

Main Results:

  • Multi-CSAR demonstrated superior performance compared to Ragout and MeDuSa on real datasets.
  • Improvements were observed in sensitivity, precision, F-score, genome coverage, NGA50, scaffold number, and running time.
  • The tool effectively scaffolds draft genomes using multiple reference genomes, even if incomplete.

Conclusions:

  • Multi-CSAR is an efficient multiple reference-based scaffolder for producing accurate genome scaffolds.
  • The tool can utilize multiple complete and/or incomplete genomes of related organisms.
  • Multi-CSAR is available as a stand-alone program for download.