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HapEdit: an accuracy assessment viewer for haplotype assembly using massively parallel DNA-sequencing technologies
Jong Hyun Kim1, Woo-Cheol Kim, Lei M Li
1Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
Nucleic Acids Research
|May 18, 2011
Summary
HapEdit is a new tool for manually correcting errors in assembled human haplotypes. This tool improves the accuracy of haplotype data derived from personal genome sequencing for disease studies.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Massively parallel sequencing technologies have reduced the cost of personal human genome sequencing.
- Haplotype assembly from personal genomes is a valuable tool for human disease research.
- Computational haplotype assembly, while accurate, contains inherent errors.
Purpose of the Study:
- To present HapEdit, a novel tool for assessing and manually editing assembled haplotypes.
- To enable users to improve the accuracy of haplotype data for downstream applications.
Main Methods:
- HapEdit allows users to break erroneous haplotype segments or concatenate supported segments.
- The tool facilitates manual editing of bases with low-quality scores.
- HapEdit provides a user-friendly interface for navigating and pinpointing regions of interest in haplotype assemblies.
- It accepts reads from various sequencing technologies including Polonator, Illumina, SOLiD, 454, and Sanger.
Main Results:
- HapEdit provides a mechanism for manual quality control and correction of assembled haplotypes.
- The tool supports the integration of data from diverse sequencing platforms.
Conclusions:
- HapEdit enhances the reliability of haplotype data derived from personal genome sequencing.
- Manual editing with HapEdit can improve the utility of assembled haplotypes for human disease studies.
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