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A natural encoding of genetic variation in a Burrows-Wheeler Transform to enable mapping and genome inference

Abstract:

We show how positional markers can be used to encode genetic variation within a Burrows-Wheeler Transform (BWT), and use this to construct a generalisation of the traditional “reference genome”, incorporating known variation within a species. Our goal is to support the inference of the closest mosaic of previously known sequences to the genome(s) under analysis. Our scheme results in an increased alphabet size, and by using a wavelet tree encoding of the BWT we reduce the performance impact o...

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Publication status:
Published
Peer review status:
Peer reviewed
Version:
Accepted manuscript

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Publisher copy:
10.1007/978-3-319-43681-4_18

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Institution:
University of Oxford
Department:
Oxford, MSD, NDM, Human Genetics Wt Centre
More by this author
Institution:
University of Oxford
Department:
Oxford, MSD, NDM, Human Genetics Wt Centre
More by this author
Institution:
University of Oxford
Department:
Oxford, MSD, NDM, Human Genetics Wt Centre
More by this author
Institution:
University of Oxford
Department:
Oxford, MSD, NDM, Human Genetics Wt Centre
Publisher:
Springer Verlag Publisher's website
Publication date:
2016-08-05
Acceptance date:
2016-05-31
DOI:
ISSN:
0302-9743
URN:
uuid:14d555a2-5f01-48f6-8ae0-7adebf6918a7
Source identifiers:
630012
Local pid:
pubs:630012

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