What is a pipeline?

Bioinformatics pipelines transform raw data into processed data that can be analyzed & visualized in Pluto

We're glad you asked! Broadly speaking, a "pipeline" or "workflow" refers to a set of steps that transform raw data into a processed format.

For an RNA-seq or other sequencing-based experiment, for example, this could involve converting a set of FASTQ files into a combined matrix (i.e. table) that contains the raw counts for each gene in each sample.