NeatSeq-Flow: A Lightweight Software for Efficient Execution of High Throughput Sequencing Workflows.

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What is NeatSeq-Flow?

  • A bioinformatics workflow (WF) is a series of computer programs called sequentially, sometimes on hundreds or even thousands of samples.
  • NeatSeq-Flow creates human readable and self explanatory shell scripts for execution on computer grids.
  • The hyrachically-organised scripts are then executed by running a master-script.
  • The main benefits in using NeatSeq-Flow are:
    • the user has full control over the WF execution;
    • the cluster job scheduler ensures correct execution order and enforces dependencies;
    • simple, cross-platform installation;
    • scripts and output files are neatly organized;
    • utilization of cluster parallelization capabilities;
    • documentation, version control as well as time & memory usage reports and
    • adding modules and expanding existing WFs requires only basic python skills.
  • NeatSeq-Flow is available on github (See Download and Install)
  • A GUI is available for parameter and sample file editting and NeatSeq-Flow execution.


While a basic number of modules come with NeatSeq-Flow, the main source of modules is the NeatSeq-Flow module and workflow repository. This repository is available on github. Check out the list of modules in the modules repository.


  • Menachem Sklarz
  • Liron Levin
  • Michal Gordon
  • Vered Chalifa-Caspi

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