NEATSEQ-FLOW: A LIGHTWEIGHT SOFTWARE FOR EASY DESIGN AND EXECUTION OF COMPLEX HIGH-THROUGHPUT SEQUENCING WORKFLOWS FOR PROGRAMMERS AND NON-PROGRAMMERS ALIKE

Nowadays, it has become almost a necessity for many biologists to execute bioinformatics workflows (WFs) as part of their research. However, most WF-management software require for their operation at least some programming expertise. Here we present NeatSeq-Flow, a platform that enables users with no programming knowledge to design and execute complex high throughput sequencing WFs. NeatSeq-Flow is easy to install and use. It can be operated either through a graphical user interface (GUI) or through the command line. A repository of over 100 pre-built modules is freely available for download, and in addition, a generic module is provided. Custom-made modules may easily be generated using templates and only basic Python programming abilities. NeatSeq-Flow is designed to enable easy sharing of WFs and modules by conceptually separating modules, WF design, sample information and execution. Moreover, NeatSeq-Flow works hand in hand with CONDA environments for easy installation of the WF`s analysis programs in one go. NeatSeq-Flow enables efficient WF execution on computer clusters by parallelizing on both samples and WF steps. NeatSeq-Flow operates by shell-script generation, thus it allows full transparency of the WF process. NeatSeq-Flow offers real-time WF execution monitoring, detailed documentation and self-sustaining WF backups for reproducibility. All of these features make NeatSeq-Flow an easy-to-use WF platform while not compromising for flexibility, reproducibility, transparency and efficiency.

NeatSeq-Flow: http://neatseq-flow.readthedocs.io/en/latest/

NeatSeq-Flow GUI: https://github.com/bioinfo-core-BGU/NeatSeq-Flow-GUI

Module and workflow repository: http://neatseq-flow.readthedocs.io/projects/neatseq-flow-modules/en/latest/

Contact: sklarz@bgu.ac.il