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All figures (17)
Table 6. Average of reconstruction rate for haplotypes with length 100.
Fig 2. The workflow of proposed method.
Table 7. Average of reconstruction rate for haplotypes with length 350.
Table 8. Average of reconstruction rate for haplotypes with length 700.
Table 5. The reconstruction rate and running time for the proposed method, H-pop, SCGD, HG, ARO and FCM applied to the experimental dataset NA12878 dataset provided by 1000 genome project.
Table 4. The effect of refinement phase for haplotypes with length 700 in diploid case.
Table 3. Average of reconstruction rate for haplotypes with length 700.
Fig 4. Partitioning Ht of a three ploid genome. The yellow parts indicate Ht 1 and the green parts demonstrate Ht 2 . It must be pointed out that Ht 1 ¼ Ht 1;1 [ Ht 1;2 [ Ht 1;3 .
Fig 5. An example of updating the current haplotype based on the partitioning of the hypergraph.
Fig 3. An example of constructing and partitioning the hypergraph. Si corresponds with the ith SNP, and the curves demonstrate the hyperedges. C1 and C2 denote the clusters which are obtained by hypergraph partitioning.
Table 1. Average of reconstruction rate for haplotypes with length 100.
Table 2. Average of reconstruction rate for haplotypes with length 350.
Fig 6. The algorithm of improving Ht.
Fig 7. Two combinations of six possible combinations of the CutSet in three ploid form.
Fig 1. An example of SNP matrices X and H relevant to the resulting haplotypes. The red measures in X indicate sequencing errors. Each row of H demonstrates a specified haplotype sequence.
Fig 8. Comparison of reconstruction rate of the methods over high coverage data a) Diploid b) Polyploid.
Table 9. The effect of refinement phase for haplotypes with length 700 in polyploid case.
Posted Content
•
DOI
•
A chaotic viewpoint-based approach to solve haplotype assembly using hypergraph model
[...]
Mohammad Hossein Olyaee
,
Alireza Khanteymoori
1
,
Khosrow Khalifeh
2
•
Institutions (2)
University of Freiburg
1
,
University of Zanjan
2
01 Oct 2020
-
bioRxiv