Going local with your data: generating FASTQ files independently of Illumina’s BaseSpace

Processing of high throughput sequence data using cloud-based applications, such as Illumina’s BaseSpace, can be computationally demanding. The process also requires manual file transfers between BaseSpace, a local computer, and high performance computing servers, which may be inefficient for diagnostic or public health laboratories providing time-sensitive genomic analyses. Therefore, we have developed a readily deployable local working environment that removes the dependence on BaseSpace for generating FASTQ files. We outline our workflow that reduces file processing times from upwards of 10 hours to approximately 30 minutes, and present comprehensive validation data for sequences generated using the Illumina MiSeq and NextSeq 500 platforms.