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The four clusters dominated by rotational velocities provide large inner variances, but also large outer distances to their neighbours (Figure 7D).
We get four clusters that provide large variances within their assigned data (inner distance), but also large (outer) distances to the nearest neighbouring centroid.
Performance does not improve when bisection stimuli with different outer distances are presented interleaved trial by trial, i.e. roving [18] [20].
In all of the clusters, except the red one, these decreases overcompensate the also occurring decreases in the outer distances between the clusters, resulting in higher cluster qualities.
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The unit of the outer distance is kb.
The maximum outer distance for a correct read pair was set to 5000 for SOLiD and 250 for GA.
A91 sequences were aligned against the reference A. nidulans genome sequence [23], [65], obtained from the Broad Institute [38] using MAQ v 0.7.1 [66] with default parameters, except for the maximum outer distance for a correct pair (-a, set to 1500) and the maximum number of mismatched that can always be found (-n, set to 3).
Height was measured from the apex of the SAM to the width line, and arc length traced the outer distance from the apex to the P1 cleft.
We sample the insert size (outer distance between the two paired reads) in base pairs from a normal distribution with mean μ = 250 and standard deviation σ = 30.
Based on these criteria, we found that the best assemblies were produced from the library with the tightest fragment size distribution and small fragments (library 24; mean outer distance of 163 bp; table 1).
We used wgsim (https://github.com/lh3/wgsim) to simulate sequencing reads from the generated target genome by setting the outer distance between the two ends to 500, standard deviation to 50, base error rate to 0.02 and the point mutation rate to 0.001 without allowing additional indel mutations.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com