Journal
NATURE REVIEWS GENETICS
Volume 13, Issue 1, Pages 36-46Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/nrg3117
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Funding
- NHGRI NIH HHS [R01 HG006677, R01 HG006102-02, R01 HG006677-12, R01 HG006102, R01 HG006102-01, R01 HG006677-13] Funding Source: Medline
- NIGMS NIH HHS [R01 GM083873] Funding Source: Medline
- NATIONAL HUMAN GENOME RESEARCH INSTITUTE [R01HG006677, R01HG006102] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM083873] Funding Source: NIH RePORTER
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Repetitive DNA sequences are abundant in a broad range of species, from bacteria to mammals, and they cover nearly half of the human genome. Repeats have always presented technical challenges for sequence alignment and assembly programs. Next-generation sequencing projects, with their short read lengths and high data volumes, have made these challenges more difficult. From a computational perspective, repeats create ambiguities in alignment and assembly, which, in turn, can produce biases and errors when interpreting results. Simply ignoring repeats is not an option, as this creates problems of its own and may mean that important biological phenomena are missed. We discuss the computational problems surrounding repeats and describe strategies used by current bioinformatics systems to solve them.
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