Search Results for "benchmark"

Counts NGS read alignments against GTF annotations in a multithreaded and scalable fashion. Benchmark: 8 core 1M annotations for 2Gb sorted reads ~30 seconds compared to ~28 minutes for bedtools multicov. Files include: fast_count_multi - reports all counts and RPKM, multithreading support fast_count_deseq - reports gene counts in deseq compatible format, multithreading support fast_count - reports all counts with no multithreading support.

...Using CONLL-Evaluation: processed 32065 tokens with 3656 phrases; found: 3251 phrases; correct: 2786. accuracy: 95.25%; precision: 85.70%; recall: 76.20%; FB1: 80.67 Using GATE Corpus Benchmark: Strict: P: 0.65 R: 0.73 F1: 0.69 Lenient: P: 0.74 R: 0.84 F1: 0.78 The details of how to reproduce evaluation, see README. To use standalone version for tagging download DrugExtractionStandalone.tar.gz from Files.

We introduce ARDEN (Artificial Reference Driven Estimation of false positives in NGS data), a novel benchmark that estimates error rates based on real experimental reads and an additionally generated artificial reference genome. It allows the computation of error rates specifically for a dataset and the construction of a ROC-curve. Thereby, it can be used to optimize parameters for read mappers, to select read mappers for a specific problem or also to filter alignments based on quality estimation.

GeneNetWeaver (GNW) is an open-source tool for in silico benchmark generation and performance profiling of network inference methods. GNW was used to generate the community-wide DREAM3, DREAM4 and DREAM5 In Silico Challenges.

TRMSim-WSN (Trust and Reputation Models Simulator for Wireless Sensor Networks) is a Java-based simulator aimed to test Trust and Reputation models for WSNs. It provides several Trust and Reputation models and new ones can be easily added.