Repository for the Cortex-based pipeline we are setting up to enter the "2015 Rapid NGS Bioinformatic Pipelines for Enhanced Molecular Epidemiologic Investigation of Pathogens"
"We" = Henk denBakker, Zam Iqbal, Phelim Bradley, Jen Gardy, Rachel Norris, Sarah Walker, Derrick Crook, Tim Peto
Given a new set of fastq, called the "challenge" for the moment, Outbryk will:
Outbryk is not ready for outside use, but feel free to take a look, and trial it if you wish. We need to make it more robust before we push it out, but the ASM NGS challenge has been a very useful trial