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 language | English (US) |
|---|---|
| Pages (from-to) | 1171-1176 |
| Number of pages | 6 |
| Journal | Computers in Biology and Medicine |
| Volume | 43 |
| Issue number | 9 |
| DOIs | |
| State | Published - Sep 1 2013 |
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Keywords
- Alignment
- Annotation
- Data analysis
- DNA
- Genotype calling
- Next generation sequencing
ASJC Scopus subject areas
- Computer Science Applications
- Health Informatics
Cite this
NGSPE : A pipeline for end-to-end analysis of DNA sequencing data and comparison between different platforms. / Huang, Ke; Yellapantula, Venkata; Baier, Leslie; Dinu, Valentin.
In: Computers in Biology and Medicine, Vol. 43, No. 9, 01.09.2013, p. 1171-1176.Research output: Contribution to journal › Article
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TY - JOUR
T1 - NGSPE
T2 - A pipeline for end-to-end analysis of DNA sequencing data and comparison between different platforms
AU - Huang, Ke
AU - Yellapantula, Venkata
AU - Baier, Leslie
AU - Dinu, Valentin
PY - 2013/9/1
Y1 - 2013/9/1
N2 - 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.
AB - 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.
KW - Alignment
KW - Annotation
KW - Data analysis
KW - DNA
KW - Genotype calling
KW - Next generation sequencing
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UR - http://www.scopus.com/inward/citedby.url?scp=84880022230&partnerID=8YFLogxK
U2 - 10.1016/j.compbiomed.2013.05.025
DO - 10.1016/j.compbiomed.2013.05.025
M3 - Article
C2 - 23930810
AN - SCOPUS:84880022230
VL - 43
SP - 1171
EP - 1176
JO - Computers in Biology and Medicine
JF - Computers in Biology and Medicine
SN - 0010-4825
IS - 9
ER -