A Lightweight Software for Efficiant Construction and Execution of High Throughput Sequencing Workflows

NeatSeq-Flow is a cross-platform, easy-to-install, lightweight python package that manages the creation and execution of workflows on computer clusters. The software is primarily used for high throughput sequencing data analysis, but it can accomodate other types of data analysis just as well.

NeatSeq-Flow receives a parameter file in YAML format and creates a hierarchy of shell scripts, which may then be executed through running a master script. This ensures full transparency, ducomentation and reproducibility of the workflow. Alternatively, the user is offered a friendly GUI which guides him/her through building the workflow and then executes it. 

The user has full control over the execution process, and he/she may execute the workflow either entirely automatically, step-by-step or even sample-by-sample.

Adding modules to NeatSeq-Flow and creating new workflows is a straighforward process, and can be achieved by anyone with basic knowledge of phython, based on existing templates.

NeatSeq -Flow is routinely used in our Bioinformatics Core Facility in many types of analyses, such as DNA assembly and annotation, RNA-Seq, ChIP-Seq, variant detection, comparative genomics, microbial typing and phylogeny, metagenomics and more.

Read More

Article at bioRxiv​

ISMB 2017 Poster at F1000

NeatSeq-Flow Documentation at Read the Docs

Learn how to use NeatSeq-Flow through a friendly Graphical User Interface (GUI) - NeatSeq-Flow GUI Tutorial

Download and Install

Download NeatSeq-Flow from GitHub

Download NeatSeq-Flow GUI from GitHub

Installation instructions: Read the Docs


Menachem Y. Sklarz, Liron Levin, Michal Gordon and Vered Chalifa-Caspi (2017) NeatSeq-Flow: A Lightweight High Throughput Sequencing Workflow Platform for Non-Programmers and Programmers Alike. bioRxiv doi: 10.1101/173005​


Menachem Sklarz,