Software pipelines: the good, the bad, and the ugly
It is now clear the impact that the revolution started by High Throughput Sequencing (HTS) had in Clinical Microbiology. These novel technologies allow us to create draft genomes in a matter of days for the approximate same cost of sequencing a dozen of genes using Sanger technology. However, in order to create those draft genomes or extract the data from the millions of reads created by HTS, researchers are confronted with a plethora of software pipelines. The choice of the pipeline to use can have significant impact on the results since from the reads to actionable results such as determination of antibiotic resistance profiles, strain lineage or presence of virulence factors, are always dependent on the software parameters and databases used. In this talk some software pipelines will be presented and their advantages and caveats discussed.