NGSANE: a lightweight production informatics framework for high-throughput data analysis.
CONCLUSIONS
The initial steps in the analysis of next-generation sequencing data can be automated by way of software 'pipelines'. However, individual components depreciate rapidly because of the evolving technology and analysis methods, often rendering entire versions of production informatics pipelines obsolete. Constructing pipelines from Linux bash commands enables the use of hot swappable modular components as opposed to the more rigid program call wrapping by higher level languages, as implemented in comparable published pipelining systems. Here we present Next Generation Sequencing ANalysis for Enterprises (NGSANE), a Linux-based, high-performance-computing-enabled framework that minimizes overhead for set up and processing of new projects, yet maintains full flexibility of custom scripting when processing raw sequence data.


METHODS
Ngsane is implemented in bash and publicly available under BSD (3-Clause) licence via GitHub at https://github.com/BauerLab/ngsane.


BACKGROUND
Denis.Bauer@csiro.au


BACKGROUND
Supplementary data are available at Bioinformatics online.
Cancer Epigenetics Program, Cancer Research Division, Kinghorn Cancer Centre, Garvan Institute of Medical Research, RNA Biology and Plasticity Laboratory, Garvan Institute of Medical Research, St Vincent's Clinical School, University of NSW, Sydney 2010, Australia and Division of Computational Informatics, CSIRO, Sydney 2113, Australia.
Fabian A
FA
Buske
Hugh J
HJ
French
Martin A
MA
Smith
Susan J
SJ
Clark
Denis C
DC
Bauer
D057205:Automation, Laboratory; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D012984:Software