IntroductionΒΆ

rnaseqflow is an open-source Python package written to make preprocessing RNAseq files more convenient. It continues to be developed actively and is in the early stages of development. It provides the ability to automate and pipeline several operations that would otherwise be performed manually.

rnaseqflow currently supports the following operations:
  • Discovery of files using recursive directory search with extension matching
  • Merging files using intelligent filename pattern matching
  • Trimming adapter sequences using fastq-mcf, either in single- or paired-end mode

These operations may be chained together, with one operation acting on the files found or created by the previous operation, to create a complete preprocessing workflow.

rnaseqflow is composed of two parts: a command line interface and a Python package. See the respective pages for information on how to use rnaseqflow.

rnaseqflow is constantly expanding and being developed, with more operations to be supported. To request support for a specific operation, request a feature, or report a bug, please create an issue at the GitHub repository below.

GitHub repository: jarvis-lab-rnaseq-flow

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