I am in process of validating a pipeline for data pre-processing, align to reference and variant calling. I am interested in using the PhiX data from Basespace. But I can not find the raw sequence forward and reverse reads anywhere on Basespace. How can I obtain the Paired end data for both MiSeq and NextSeq platform to use as input files for the pipeline?
The purpose of the pipeline is to work on bacterial and viral genomes to find variants.
Are there any other gold standard databases to use to validate the pipeline?