Adapter prediction performance at different parameter settings on the 539 small RNA libraries.

<p><b>A</b>: Adapter prediction performance on raw reads (left) and trimmed reads with Phred score cutoff ≥ 10 (Q10; center) and ≥ 20 (Q20; right) is shown at different <i>k</i> and <i>R</i> parameter settings. The parameter combination with the best performance (<i>k</i> = 9 and <i>R</i> = 1.4) is highlighted with a larger cyan circle in the left panel. <b>B</b>: Adapter prediction performance on raw reads is shown with low complexity <i>k</i>-mers filtered out (left) and without the filtering step (right). The numbers in the panels indicate the number of correctly predicted adapters.</p

Quality score distribution and highly abundant small RNAs for the three libraries that Minion failed to predict the correct adapters.

<p>The distributions of quality scores for the three libraries that Minion wrongly predicted the 3´ adapter sequences are shown in three panels in the top row. Highly abundant small RNA species sequenced in the three libraries are shown in the middle row, and the wrongly predicted 3´ adapter sequences with Minion using 9-mer as the parameter are shown in the bottom row. The correct 3´ adapter sequences (8-nt long) and the parts of the highly abundant small RNA sequences are colored in blue and red respectively.</p

Adapter prediction performance of DNApi and Minion on the 539 small RNA libraries.

<p><b>A</b>: Averaged memory usage and runtime of DNApi and Minion in different <i>k</i>-mer settings across all libraries are shown. The <i>iterative</i> mode in DNApi was run with <i>k</i> ∈ {9, 11}. <b>B</b>: Memory usage and runtime of DNApi and Minion in individual small RNA libraries are shown. <i>k</i> = 9 for the left panels and <i>k</i> = 12 for the right panels. The X-axis shows the sequencing depth of a library (total number of reads). The Y-axis of the upper panels is runtime in seconds and the Y-axis of the lower panels is memory usage in megabytes. Each library is shown as a symbol (circle and square for DNApi and triangle for Minion) with the size of the symbol indicating the read length of the library.</p

Adapter prediction algorithm workflow.

<p>Adapter prediction algorithm workflow.</p

ISR’s for funnel properties obtained using angular distance or RMSD.

<p>N is the number of the closest neighbors used to calculate the properties. The best prediction for each property is in bold.</p

Success rate for the standard 6° rotational sampling and the hybrid-resolution approach.

<p>Success rate for the standard 6° rotational sampling and the hybrid-resolution approach.</p

Angular and RMSD distances between the first ZDOCK prediction of 1BJ1 and the top 1000 and bottom 1000 predictions.

<p>The optimal clustering corresponds to 19° angular distance pruning and 6 Å RMSD pruning.</p

Average hit count for the standard 6° rotational sampling and the hybrid-resolution approach.

<p>Average hit count for the standard 6° rotational sampling and the hybrid-resolution approach.</p

Success rate for 15° and 6° rotational sampling, and for 6° rotational sampling with 19° angular distance pruning or 6 Å RMSD pruning.

<p>Success rate for 15° and 6° rotational sampling, and for 6° rotational sampling with 19° angular distance pruning or 6 Å RMSD pruning.</p

IRMSD’s of the best predictions for the standard 6° rotational sampling run and the hybrid-resolution run, for the top 100 (top panel) and top 1000 (bottom panel) predictions.

<p>IRMSD’s of the best predictions for the standard 6° rotational sampling run and the hybrid-resolution run, for the top 100 (top panel) and top 1000 (bottom panel) predictions.</p