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Evaluating performance of metagenomic characterization algorithms using in silico datasets generated with FASTQSim.
Fig. 1 Overview of the activity, attenuation and anatomical datasets generated with the XCAT phantom.
The resulting images were evaluated against the ground truth represented by the resampled original datasets generated with the XCAT software.
We have chosen the truncation point at p=10 because datasets generated with p=10 or with p close to 10 have similar statistical behavior.
However, there was a statistically significant difference in 1.5-fold AUC between datasets generated with aRNA targets and datasets generated with ss-cDNA targets (P < 0.01).
We also performed paired-ended assemblies using ABYSS on datasets generated with mate-pairs information.
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The accuracy of the final point cloud generated with the system was tested in two modes through a comparison with a dataset generated with a close range 3D colour laser scanner.
The same pattern was observable when analyzing the case-control dataset generated with the PM2 phenocopy method (see Supplementary Figure S3).
The consensus secondary structure of our dataset, generated with RNAsalsa, can be understood as a model parameter that defines site interactions and thus character dependence due to compensatory mutations [ 34, 82, 83].
"Win64-2" denotes a machine with a 2.3 Ghz Intel Celeron G1610T processor (2 cores) and 8GB RAM running 64-bit Windows 8. "synth1" refers to a 1000 sample, 100000 variant synthetic dataset generated with HAPGEN2 [ 37 ], while "synth1p" refers to the same dataset after one round of –indep-pairwise 50 5 0.5 pruning (with 76124 markers remaining).
Both datasets generated models with a coefficient of determination (R) of 0.8 (share of explained variability, Figure 3A B).
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