Benchmarking Foodborne Pathogen Assemblies

Four of the most common foodborne pathogen species are Salmonella Enterica, Listeria Monocytogenes, Escherichia coli and Shigella, and Campylobacter. From SRA, we randomly selected 5500 read sets from these species sequenced on Illumina machines, sorted them by number of bases in reads, and dropped 250 runs each with lowest and highest base counts. The remaining 5000 reads sets used as the random set have 3306 Salmonella, 428 Listeria, 773 Escherichia, 148 Shigella, and 345 Campylobacter. These sets were used to test the contiguity of assemblies. Runs for the random set were done in an uncontrolled environment on compute farm. We note that the CPU times reported by the compute farm (data not shown) on these 5000 read sets corroborate the run time performance presented in Table 1.