vargas-experiments

small_test

Small test dataset for testing Vargas

Scaling Experiments (Section 3.1)

Generating graphs and read sets to test thread scaling on Knights Landing and Skylake architectures with SSE4.1, AVX2, and AVX512BW instruction sets

Heuristic Experiments (Section 3.2-3.3)

Aligning reads with the scoring function of popular aligners to evaluate alignment correctness and mapping quality

###Optimization Experiments (Section 4 and Supplementary Information)

Optimizing Bowtie 2 parameters for aligning datasets of ChIP-seq reads (chipseq) and 100bp WGS reads (100bp).