SIMPLEX: cloud-enabled pipeline for the comprehensive analysis of exome sequencing data

In recent studies, exome sequencing has proven to be a successful screening tool for the identification of candidate genes causing rare genetic diseases. Although underlying targeted sequencing methods are well established, necessary data handling and focused, structured analysis still remain demanding tasks. Researchers at division for bioinformatics, biocenter, Innsbruck Medical University, Innsbruck, Austria,  developed a cloud-enabled autonomous analysis pipeline, which comprises the complete exome analysis workflow.

The pipeline combines several in-house developed and published applications to perform the following steps:

(a) initial quality control,

(b) intelligent data filtering and pre-processing,

(c) sequence alignment to a reference genome,

(d) SNP and DIP detection,

(e) functional annotation of variants using different approaches, and

(f) detailed report generation during various stages of the workflow.

The pipeline connects the selected analysis steps, exposes all available parameters for customized usage, performs required data handling, and distributes computationally expensive tasks either on a dedicated high-performance computing infrastructure or on the Amazon cloud environment (EC2). The presented application has already been used in several research projects including studies to elucidate the role of rare genetic diseases. The pipeline is continuously tested and is publicly available under the GPL as a VirtualBox or Cloud image at http://simplex.i-med.ac.at .

Reference:
Fischer M, Snajder R, Pabinger S, Dander A, Schossig A, et al. (2012) SIMPLEX: Cloud-Enabled Pipeline for the Comprehensive Analysis of Exome Sequencing Data. PLoS ONE 7(8): e41948. doi:10.1371/journal.pone.0041948

Incoming search terms:

  • simplex cloud
  • R summary illumina exome chip
  • r package for exome sequencing pipeline
  • r package for exome sequencing
  • pipeline for exome sequencing
  • mapreduce simplex
  • map reduce simplex
  • exome rna-seq
  • exom sequencing mapping pipeline
  • chip sequencing analysis AND PLoS ONE

Subscribe NGS Updates

Share This Article

You might also like

Leave a Reply

Submit Comment

© 2024 Genomics Gateway. All rights reserved.