A survey of tools for variant analysis of next-generation genome sequencing data
Recent advances in genome sequencing technologies provide unprecedented opportunities to characterize individual genomic landscapes and identify mutations relevant for diagnosis and therapy. Specifically, whole-exome sequencing using next-generation sequencing (NGS) technologies is gaining popularit...
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Published in | Briefings in bioinformatics Vol. 15; no. 2; pp. 256 - 278 |
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Main Authors | , , , , , , , , , |
Format | Journal Article |
Language | English |
Published |
England
Oxford Publishing Limited (England)
01.03.2014
Oxford University Press |
Subjects | |
Online Access | Get full text |
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Abstract | Recent advances in genome sequencing technologies provide unprecedented opportunities to characterize individual genomic landscapes and identify mutations relevant for diagnosis and therapy. Specifically, whole-exome sequencing using next-generation sequencing (NGS) technologies is gaining popularity in the human genetics community due to the moderate costs, manageable data amounts and straightforward interpretation of analysis results. While whole-exome and, in the near future, whole-genome sequencing are becoming commodities, data analysis still poses significant challenges and led to the development of a plethora of tools supporting specific parts of the analysis workflow or providing a complete solution. Here, we surveyed 205 tools for whole-genome/whole-exome sequencing data analysis supporting five distinct analytical steps: quality assessment, alignment, variant identification, variant annotation and visualization. We report an overview of the functionality, features and specific requirements of the individual tools. We then selected 32 programs for variant identification, variant annotation and visualization, which were subjected to hands-on evaluation using four data sets: one set of exome data from two patients with a rare disease for testing identification of germline mutations, two cancer data sets for testing variant callers for somatic mutations, copy number variations and structural variations, and one semi-synthetic data set for testing identification of copy number variations. Our comprehensive survey and evaluation of NGS tools provides a valuable guideline for human geneticists working on Mendelian disorders, complex diseases and cancers. |
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AbstractList | Recent advances in genome sequencing technologies provide unprecedented opportunities to characterize individual genomic landscapes and identify mutations relevant for diagnosis and therapy. Specifically, whole-exome sequencing using next-generation sequencing (NGS) technologies is gaining popularity in the human genetics community due to the moderate costs, manageable data amounts and straightforward interpretation of analysis results. While whole-exome and, in the near future, whole-genome sequencing are becoming commodities, data analysis still poses significant challenges and led to the development of a plethora of tools supporting specific parts of the analysis workflow or providing a complete solution. Here, we surveyed 205 tools for whole-genome/whole-exome sequencing data analysis supporting five distinct analytical steps: quality assessment, alignment, variant identification, variant annotation and visualization. We report an overview of the functionality, features and specific requirements of the individual tools. We then selected 32 programs for variant identification, variant annotation and visualization, which were subjected to hands-on evaluation using four data sets: one set of exome data from two patients with a rare disease for testing identification of germline mutations, two cancer data sets for testing variant callers for somatic mutations, copy number variations and structural variations, and one semi-synthetic data set for testing identification of copy number variations. Our comprehensive survey and evaluation of NGS tools provides a valuable guideline for human geneticists working on Mendelian disorders, complex diseases and cancers. Recent advances in genome sequencing technologies provide unprecedented opportunities to characterize individual genomic landscapes and identify mutations relevant for diagnosis and therapy. Specifically, whole-exome sequencing using next-generation sequencing (NGS) technologies is gaining popularity in the human genetics community due to the moderate costs, manageable data amounts and straightforward interpretation of analysis results. While whole-exome and, in the near future, whole-genome sequencing are becoming commodities, data analysis still poses significant challenges and led to the development of a plethora of tools supporting specific parts of the analysis workflow or providing a complete solution. Here, we surveyed 205 tools for whole-genome/whole-exome sequencing data analysis supporting five distinct analytical steps: quality assessment, alignment, variant identification, variant annotation and visualization. We report an overview of the functionality, features and specific requirements of the individual tools. We then selected 32 programs for variant identification, variant annotation and visualization, which were subjected to hands-on evaluation using four data sets: one set of exome data from two patients with a rare disease for testing identification of germline mutations, two cancer data sets for testing variant callers for somatic mutations, copy number variations and structural variations, and one semi-synthetic data set for testing identification of copy number variations. Our comprehensive survey and evaluation of NGS tools provides a valuable guideline for human geneticists working on Mendelian disorders, complex diseases and cancers. [PUBLICATION ABSTRACT] |
Author | Efremova, Mirjana Dander, Andreas Snajder, Rene Zschocke, Johannes Krabichler, Birgit Fischer, Maria Sperk, Michael Speicher, Michael R Trajanoski, Zlatko Pabinger, Stephan |
Author_xml | – sequence: 1 givenname: Stephan surname: Pabinger fullname: Pabinger, Stephan email: zlatko.trajanoski@i-med.ac.at organization: Division for Bioinformatics, Innsbruck Medical University, Innrain 80, 6020 Innsbruck, Austria. Tel.: +43-512-9003-71401; Fax: +43-512-9003-73100; zlatko.trajanoski@i-med.ac.at – sequence: 2 givenname: Andreas surname: Dander fullname: Dander, Andreas – sequence: 3 givenname: Maria surname: Fischer fullname: Fischer, Maria – sequence: 4 givenname: Rene surname: Snajder fullname: Snajder, Rene – sequence: 5 givenname: Michael surname: Sperk fullname: Sperk, Michael – sequence: 6 givenname: Mirjana surname: Efremova fullname: Efremova, Mirjana – sequence: 7 givenname: Birgit surname: Krabichler fullname: Krabichler, Birgit – sequence: 8 givenname: Michael R surname: Speicher fullname: Speicher, Michael R – sequence: 9 givenname: Johannes surname: Zschocke fullname: Zschocke, Johannes – sequence: 10 givenname: Zlatko surname: Trajanoski fullname: Trajanoski, Zlatko |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/23341494$$D View this record in MEDLINE/PubMed |
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Snippet | Recent advances in genome sequencing technologies provide unprecedented opportunities to characterize individual genomic landscapes and identify mutations... |
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SubjectTerms | Annotations Biotechnology Cancer Computational Biology - methods Data processing Disease - genetics DNA Copy Number Variations Exome Genetic Variation Genetics Genome, Human Genomics High-Throughput Nucleotide Sequencing - statistics & numerical data Humans Molecular Sequence Annotation Mutation Mutations Performance evaluation Reproduction Sequence Alignment - statistics & numerical data Sequence Analysis, DNA - statistics & numerical data Sequencing Software Variance analysis Visualization |
Title | A survey of tools for variant analysis of next-generation genome sequencing data |
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