Unknown

Dataset Information

0

NGSANE: a lightweight production informatics framework for high-throughput data analysis.


ABSTRACT:

Summary

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.

Availability and implementation

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

Contact

Denis.Bauer@csiro.au

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Buske FA 

PROVIDER: S-EPMC4016703 | biostudies-literature | 2014 May

REPOSITORIES: biostudies-literature

altmetric image

Publications

NGSANE: a lightweight production informatics framework for high-throughput data analysis.

Buske Fabian A FA   French Hugh J HJ   Smith Martin A MA   Clark Susan J SJ   Bauer Denis C DC   Bauer Denis C DC  

Bioinformatics (Oxford, England) 20140126 10


<h4>Summary</h4>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  ...[more]

Similar Datasets

| S-EPMC3756668 | biostudies-literature
| S-EPMC8282813 | biostudies-literature
| S-EPMC7941695 | biostudies-literature
| S-EPMC6334930 | biostudies-literature
| S-EPMC5862285 | biostudies-literature
| S-EPMC8284407 | biostudies-literature
| S-EPMC4177668 | biostudies-literature
| S-EPMC8481803 | biostudies-literature
| S-EPMC5128788 | biostudies-literature
| S-EPMC6989550 | biostudies-literature