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Other assemblers had poor performances in the accuracy of assembling repeats and nonrepeats.
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Therefore, for the accuracy of assembling repeats, SWA and SGA are the top two assemblers.
For the accuracy of assembling repeats, SWA and MSR-CA achieved the best results.
The accuracy of assembling repeats and estimating the copy numbers is up to 99% and 100%, respectively.
The addition of Illumina data also improved the accuracy of assembled contigs.
The accuracy of assembled haplotypes increased significantly after removing chimeric fragment candidates.
For comparisons in real NGS datasets, the metrics such as TRC, NNC, and Rep-size are used to evaluate the completeness of assembled repeats and nonrepeats; the metrics such as Rep-accuracy, C-accuracy, and CN-accuracy are used to evaluate the accuracy of assembled repeats and nonrepeats, while the N50, N90, and maximum contig are used to evaluate the continuity of whole genome assembly.
Rep-accuracy (Rep-acc) is the accuracy of assembled repeat contigs, which is designed to evaluate the correctness of all types of assembled repeat contigs and defined as Rep-accuracy = 1 − (∑| L a − L r |/∑ L r ), where L r represents the length of real repeat and L a represents the length of assembled repeat contig.
A number of problems, arising when mounting large-sized constructions and influencing the accuracy of assembling are considered in this article.
It was clearly shown in Table 5 that the appropriate increase of filtered times could also improve the accuracy of assembling repeats.
But for the repeats longer than read length, most of them performed poorly in completeness and accuracy of assembling repeats from NGS data.
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