Dec 19, 2014

ViennaNGS: A toolbox for building efficient next-generation sequencing analysis pipelines

BioRxiv : the Preprint Server for Biology
Michael T WolfingerFabian Amman

Abstract

Motivation Recent achievements in next-generation sequencing (NGS) technologies lead to a high demand for reuseable software components to easily compile customized analysis workflows for big genomics data. Results We present ViennaNGS, an integrated collection of Perl modules focused on building efficient pipelines for NGS data processing. It comes with functionality for extracting and converting features from common NGS file formats, computation and evaluation of read mapping statistics, quantification and normalization of read count data, identification and characterization of splice junctions from RNA-seq data, parsing and condensing sequence motif data, automated construction of Assembly and Track Hubs for the UCSC genome browser and wrapper routines for a set of commonly used NGS command line tools. Availability The ViennaNGS Perl distribution is available through CPAN and GitHub at <https://github.com/mtw/Bio-ViennaNGS>. Contact michael.wolfinger{at}univie.ac.at Supplementary Information Supplementary data for the ViennaNGS tutorial is available from <http://rna.tbi.univie.ac.at/ViennaNGS>

  • References
  • Citations

References

  • We're still populating references for this paper, please check back later.
  • References
  • Citations

Citations

  • This paper may not have been cited yet.

Mentioned in this Paper

Molecular Sequence Database
Computer Software
Genome
Evaluation
Scutovertex
Genomics
Massively-Parallel Sequencing
Protein Domain
RNA Splicing
Base Sequence

Related Feeds

BioRxiv & MedRxiv Preprints

BioRxiv and MedRxiv are the preprint servers for biology and health sciences respectively, operated by Cold Spring Harbor Laboratory. Here are the latest preprint articles (which are not peer-reviewed) from BioRxiv and MedRxiv.