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SCARPA: scaffolding reads with practical algorithms

机译:SCARPA:使用实用算法读取支架

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Results: We present SCARPA, a novel scaffolder, which combines fixed-parameter tractable and bounded algorithms with Linear Programming to produce near-optimal scaffolds. We test SCARPA on real datasets in addition to a simulated diploid genome and compare its performance with several state-of-the-art scaffolders. We show that SCARPA produces longer or similar length scaffolds that are highly accurate compared with other scaffolders. SCARPA is also capable of detecting misassembled contigs and reports them during scaffolding.
机译:结果:我们提出了一种新型的脚手架SCARPA,它将固定参数的可处理的和有界的算法与线性编程相结合,以产生接近最佳的脚手架。除了模拟的二倍体基因组外,我们还在真实数据集上测试SCARPA,并将其性能与几种最新的脚手架进行比较。我们表明,SCARPA可以生产更长或更相似长度的脚手架,与其他脚手架相比,它们是高度准确的。 SCARPA还能够检测错位的重叠群,并在脚手架中报告它们。

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