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Title
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NanoSatellite : accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION
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Author
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Abstract
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| Technological limitations have hindered the large-scale genetic investigation of tandem repeats in disease. We show that long-read sequencing with a single Oxford Nanopore Technologies PromethION flow cell per individual achieves 30× human genome coverage and enables accurate assessment of tandem repeats including the 10,000-bp Alzheimer’s disease-associated ABCA7 VNTR. The Guppy “flip-flop” base caller and tandem-genotypes tandem repeat caller are efficient for large-scale tandem repeat assessment, but base calling and alignment challenges persist. We present NanoSatellite, which analyzes tandem repeats directly on electric current data and improves calling of GC-rich tandem repeats, expanded alleles, and motif interruptions. |
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Language
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English
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Source (journal)
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Genome biology. - London, 1999, currens
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Publication
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London
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BioMed Central Ltd
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2019
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ISSN
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1474-760X
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DOI
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10.1186/S13059-019-1856-3
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Volume/pages
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20
:1
(2019)
, 16 p.
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Article Reference
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239
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ISI
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000497703300005
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Pubmed ID
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31727106
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Medium
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E-only publicatie
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Full text (Publisher's DOI)
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Full text (open access)
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