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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
Published on: April 4, 2018
Repetitive DNA and next-generation sequencing: computational challenges and solutions.
Todd J Treangen1, Steven L Salzberg
1McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
Nature Reviews. Genetics
|November 30, 2011
Summary
Repetitive DNA sequences pose significant challenges for genome assembly and alignment, especially with next-generation sequencing data. Bioinformatics strategies are crucial for accurately analyzing these abundant genomic regions.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Repetitive DNA sequences are prevalent across species, constituting a substantial portion of the human genome.
- These repeats present persistent technical hurdles for sequence alignment and assembly algorithms.
- Short read lengths and high data volumes from next-generation sequencing exacerbate these challenges.
Purpose of the Study:
- To discuss the computational problems associated with repetitive DNA sequences in genomics.
- To describe current bioinformatics strategies for addressing these challenges in sequence analysis.
Main Methods:
- Review of computational challenges in handling repetitive DNA.
- Analysis of existing bioinformatics system strategies for repeat resolution.
Main Results:
- Repetitive sequences introduce ambiguities, leading to potential biases and errors in genomic data interpretation.
- Ignoring repetitive elements can result in the omission of critical biological insights.
Conclusions:
- Effective computational strategies are essential for accurate genome assembly and analysis in the presence of repetitive DNA.
- Bioinformatics tools must be developed and refined to overcome the complexities introduced by repetitive sequences.
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