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However, the intermediate k-mer counts would need to be stored on disk, which requires significant amount of additional space, and the merge phase is not parallelized (Marais and Kingsford, 2011, User manual, Section Bugs).
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In case a merging phase is required (e.g., to provide a global filtering of the data), it is expected to be an online process on the result stream flowing to a permanent storage.
Figure 1 depicts an example of the cluster merge phase, the initial state is on the left, and the final state is on the right.
For applications where speed is more important than accuracy, the cluster merging phase can be left out.
We added a new merge phase to MapReduce that can efficiently merge data from the map and reduce modules.
The goal of the second phase is to merge clusters obtained during the previous phase, based on the repeats and information provided by the paired-end reads.
This inflection point is an appropriate initial value of the maximum diameter because the objective of the first phase is to merge the data points which are extremely close to each other and consider them collectively.
Another important phase is the group merging which includes calculating merging priority and ranking.
The computational complexity of the cluster merging phase involves merging clusters that were found using the attractor vertices.
Master phase: This phase is the complimenting phase.
The prodrome phase is the first phase.
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