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Even though potentially computationally more expensive, the meshing automation may lead to drastic time reduction for the CAD to mesh process and a much tighter link between CAD and calculated assembly.
As a result, the calculated assembly efficiency (the ratio of the number of supernatant HCV RNA copies to that of intracellular HCV RNA copies) and budding efficiency (the ratio of the HCV titer in the cell supernatant to that in cells) were similar in siRBM24- and siNC-transfected cells (Fig. 1I and 1J).
The average assembly depth estimated by calculated assembly length divided by actual assembly length was 14x (indicated by the yellow dashed line), around which large contigs were clustered.
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To characterize the behavior of a dilute assembly of random nanoparticle clusters, it is necessary to calculate assembly hysteresis loop averaged over a sufficiently large number of random cluster realizations.
Transrate v0.3.1 [ 27] was used to calculate assembly quality metrics.
We calculate assembly yields as Nt/ N, where Nt is the number of clusters with desired composition and N is the total number of clusters with the maximum number of monomers.
We clustered the resulting isotigs using Vmatch (http://www.vmatch.de; –dbcluster p small = 99 and p large = 99) to form a non-redundant set of sequences, and then calculated the assembly statistics shown in Table 2 using custom Perl scripts.
Average contig spectra were calculated using assemblies of 10,000 randomly selected sequences with enough repetitions to achieve 2× coverage of each metagenome.
COMPASS statistics were calculated for assemblies from bird and snake.
Some results from the validation process are presented: the comparison of APOLLO2.8 results to reference Monte Carlo TRIPOLI4 results on specific BWR benchmarks emphasizes the ability of the deterministic tool to calculate BWR assembly multiplication factor within 200 pcm accuracy for void fraction varying from 0 to 100%.
An alignment error profile generated by RefAligner is used with the estimated genome length to calculate default assembly parameters; and the eight other scripts that include variants of these parameters.
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