NGSPE: A pipeline for end-to-end analysis of DNA sequencing data and comparison between different platforms

Ke Huang, Venkata Yellapantula, Leslie Baier, Valentin Dinu

Research output: Contribution to journalArticle

2 Scopus citations

Abstract

We present NGSPE, a pipeline for variation discovery and genotyping of pair-ended Illumina next generation sequencing (NGS) data (http://ngspeanalysis.sourceforge.net/). This pipeline not only describes a set of sequential analytical steps, such as short reads alignment, genotype calling and functional variation annotation that can be conducted using open-source software tools, but also provides users a set of scripts to install the dependent software and resources and implement the pipeline on their data. A sample summary report including the concordance rate between data generated by this pipeline and different resources as well as the comparison between replication samples of two commercial platforms from Illumina and Complete Genomics is also provided. Furthermore, some of the mutations identified by the pipeline were verified using Sanger sequencing.

Original languageEnglish (US)
Pages (from-to)1171-1176
Number of pages6
JournalComputers in Biology and Medicine
Volume43
Issue number9
DOIs
StatePublished - Sep 1 2013

Keywords

  • Alignment
  • Annotation
  • DNA
  • Data analysis
  • Genotype calling
  • Next generation sequencing

ASJC Scopus subject areas

  • Computer Science Applications
  • Health Informatics

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