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DOI: 10.4230/LIPIcs.WABI.2018.4
URN: urn:nbn:de:0030-drops-93060
URL: https://drops.dagstuhl.de/opus/volltexte/2018/9306/
Sirén, Jouni ; Garrison, Erik ; Novak, Adam M. ; Paten, Benedict J. ; Durbin, Richard
Haplotype-aware graph indexes
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Abstract
The variation graph toolkit (VG) represents genetic variation as a graph. Each path in the graph is a potential haplotype, though most paths are unlikely recombinations of true haplotypes. We augment the VG model with haplotype information to identify which paths are more likely to be correct. For this purpose, we develop a scalable implementation of the graph extension of the positional Burrows-Wheeler transform. We demonstrate the scalability of the new implementation by indexing the 1000 Genomes Project haplotypes. We also develop an algorithm for simplifying variation graphs for k-mer indexing without losing any k-mers in the haplotypes.
BibTeX - Entry
@InProceedings{sirn_et_al:LIPIcs:2018:9306,
author = {Jouni Sir{\'e}n and Erik Garrison and Adam M. Novak and Benedict J. Paten and Richard Durbin},
title = {{Haplotype-aware graph indexes}},
booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
pages = {4:1--4:13},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-082-8},
ISSN = {1868-8969},
year = {2018},
volume = {113},
editor = {Laxmi Parida and Esko Ukkonen},
publisher = {Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
address = {Dagstuhl, Germany},
URL = {http://drops.dagstuhl.de/opus/volltexte/2018/9306},
URN = {urn:nbn:de:0030-drops-93060},
doi = {10.4230/LIPIcs.WABI.2018.4},
annote = {Keywords: FM-indexes, variation graphs, haplotypes}
}
| Keywords: | FM-indexes, variation graphs, haplotypes | |
| Seminar: | 18th International Workshop on Algorithms in Bioinformatics (WABI 2018) | |
| Issue date: | 2018 | |
| Date of publication: | 02.08.2018 | |
| Supplementary Material: | The implementation can be found at https://github.com/vgteam/vg, https://github.com/jltsiren/gbwt, and https://github.com/jltsiren/gcsa2. |
