A Survey of Computational Tools to Analyze and Interpret Whole Exome Sequencing Data
Open Access
- 14 December 2016
- journal article
- review article
- Published by Wiley in International Journal of Genomics
- Vol. 2016, 1-16
Abstract
Whole Exome Sequencing (WES) is the application of the next-generation technology to determine the variations in the exome and is becoming a standard approach in studying genetic variants in diseases. Understanding the exomes of individuals at single base resolution allows the identification of actionable mutations for disease treatment and management. WES technologies have shifted the bottleneck in experimental data production to computationally intensive informatics-based data analysis. Novel computational tools and methods have been developed to analyze and interpret WES data. Here, we review some of the current tools that are being used to analyze WES data. These tools range from the alignment of raw sequencing reads all the way to linking variants to actionable therapeutics. Strengths and weaknesses of each tool are discussed for the purpose of helping researchers make more informative decisions on selecting the best tools to analyze their WES data.Keywords
Funding Information
- National Institutes of Health (P50CA058187)
This publication has 81 references indexed in Scilit:
- A reliable method for the detection of BRCA1 and BRCA2 mutations in fixed tumour tissue utilising multiplex PCR-based targeted next generation sequencingBMC Clinical Pathology, 2015
- COSMIC: exploring the world's knowledge of somatic mutations in human cancerNucleic Acids Research, 2014
- A practical method to detect SNVs and indels from whole genome and exome sequencing dataScientific Reports, 2013
- Identifying Mendelian disease genes with the Variant Effect Scoring ToolBMC Genomics, 2013
- FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short ReadsPLOS ONE, 2012
- Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov ModelsHuman Mutation, 2012
- Fast gapped-read alignment with Bowtie 2Nature Methods, 2012
- SOAP2: an improved ultrafast tool for short read alignmentBioinformatics, 2009
- Mapping short DNA sequencing reads and calling variants using mapping quality scoresGenome Research, 2008
- KEGG: Kyoto Encyclopedia of Genes and GenomesNucleic Acids Research, 2000