Fig. 2.

Schematic illustration of the ARCHS4 cloud-based alignment pipeline workflow. A job scheduler instructs Dockerized alignment instances that are processing FASTQ files from the SRA database in parallel. The pipeline supports the STAR and Kallisto aligners. The final results are sent to a database for post-processing. Dimensionality reduction for data visualization is calculated with t-SNE, and all counts are additionally stored in a H5 data matrix. The .sra file extension is the native file format for files from the SRA database