NeatSeq-Flow: a lightweight software for efficient execution of high throughput sequencing workflows

Bioinformatics workflows (WFs) in general, and those involving High Throughput Sequencing data in particular, typically involve executing a sequence of programs on raw sequence files from as many as thousands of samples. Management of these WFs is laborious and error-prone. We have developed NeatSeq-Flow, a python package that manages WF creation for execution on computer clusters. NeatSeq-Flow creates shell scripts as well as a directory structure for storing analysis results, error messages, and execution logs. The user maintains full control over the execution of the WF, while the computer cluster enforces sequential execution and parallelization. NeatSeq-Flow also supplies tools for version tracking, documentation and execution logging.