RT Journal Article
SR Electronic
T1 NeatSeq-Flow: A Lightweight Software for Efficient Execution of High Throughput Sequencing Workflows
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 173005
DO 10.1101/173005
A1 Menachem Sklarz
A1 Michal Gordon
A1 Vered Chalifa-Caspi
YR 2017
UL http://biorxiv.org/content/early/2017/08/08/173005.abstract
AB Summary 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.Availability: https://github.com/bioinfo-core-BGU/neatseq-flowContact: sklarz{at}bgu.ac.il