If here courtesy of Bitbucket or source code, check out the docs online at: seqpipe, and the package vignette.

Where seqpipe excels is in separating processing into two distinct phases:

  • Per Sample Processing - each sample is treated independently, and processing can occur in parallel
  • Replicate-aware Processing - samples are combined into condition-specific folders such that interdependent samples can be processed together. This is particularly important for ChIP-seq where samples are paired with cognate inputs, and additionally for methods which are designed to consider replicates

Each script (see the Reference page) takes on a specific filetype or step of the process, and is labeled chronologically in alphabetical order, designed to run from A through Z.


Check out the vignette to learn more on the design and execution of the seqpipe.


For inspecting source code and downloading the latest pipeline package, navigate to the Downloads courtesy of Bitbucket.