Format

Send to

Choose Destination
Sci Rep. 2018 May 1;8(1):6793. doi: 10.1038/s41598-018-25022-6.

DNAp: A Pipeline for DNA-seq Data Analysis.

Author information

1
Department of Computer Science, Arkansas State University, Jonesboro, Arkansas, 72467, United States of America.
2
Department of Biomedical Informatics and the Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, 72205, United States of America.
3
Department of Mathematics and Computer Science, University of Arkansas at Pine Bluff, Pine Bluff, Arkansas, 55455, United States of America.
4
Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States of America.
5
Department of Information Science, University of Arkansas at Little Rock, Little Rock, Arkansas, 72204, United States of America.
6
Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109, United States of America.
7
Department of Computer Science, Arkansas State University, Jonesboro, Arkansas, 72467, United States of America. xhuang@astate.edu.

Abstract

Next-generation sequencing is empowering genetic disease research. However, it also brings significant challenges for efficient and effective sequencing data analysis. We built a pipeline, called DNAp, for analyzing whole exome sequencing (WES) and whole genome sequencing (WGS) data, to detect mutations from disease samples. The pipeline is containerized, convenient to use and can run under any system, since it is a fully automatic process in Docker container form. It is also open, and can be easily customized with user intervention points, such as for updating reference files and different software or versions. The pipeline has been tested with both human and mouse sequencing datasets, and it has generated mutations results, comparable to published results from these datasets, and reproducible across heterogeneous hardware platforms. The pipeline DNAp, funded by the US Food and Drug Administration (FDA), was developed for analyzing DNA sequencing data of FDA. Here we make DNAp an open source, with the software and documentation available to the public at http://bioinformatics.astate.edu/dna-pipeline/ .

Supplemental Content

Full text links

Icon for Nature Publishing Group Icon for PubMed Central
Loading ...
Support Center