Higher quality metrics value represents the better cluster quality.
In the assembly of UCREL1 dataset (see Table-S4; Additional file 1), ABySS, IDBA-UD, and SPAdes exhibit high quality g1 metrics performance, which is better than the performance of the current draft genome (df_1) at the contigs level, while ABySS, IDBA-UD, SPAdes and Velvet have better g1 metrics performance than df_1 at the scaffolds level (see Fig. S4; Additional file 2).
The study shows a high correlation of fingerprint quality metrics among themselves.
Even though the number of proteins assigned to each EC number is very unbalanced, the majority of classes were classified properly, with high quality according to the metrics extracted.
Summarizing, we perform a systematic study on a high quality ChEMBL dataset, using two metrics for validation Mathews Correlation Coefficient (MCC) and Boltzmann-Enhanced Discrimination of ROC (BEDROC).
The Pacific region had especially high article output relative to both GDP and population, as well as high quality articles, based on citation metrics.
Additionally, we run the assembler tools several times (except for IDBA-UD and SPAdes) with different k-mer parameter and choose the optimal value for k that exhibits high quality of g1 and g2 metrics.
Since WES/WGS is not targeting specific diseases/genes, the validation effort is not focused on the specific sequence contexts and variant types associated with those diseases, but rather on developing and evaluating end-to-end metrics for high quality sequencing.
The Data Summary reports, for each input file, the total amount of short reads (both raw and high quality reads as filtered by NGS QC Toolkit), mapping metrics, junctions alignment metrics and information from poly(A) extraction phase.
According to these quality metrics, the higher is the IOSNR, and the lower is the MAE, the better is the improvement of the image enhanced/reconstructed with the particular employed algorithm.
