1 Search Results for "Novak, Adam M."


Document
Haplotype-aware graph indexes

Authors: Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict J. Paten, and Richard Durbin

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)


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.

Cite as

Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict J. Paten, and Richard Durbin. Haplotype-aware graph indexes. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 4:1-4:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)


Copy BibTex To Clipboard

@InProceedings{siren_et_al:LIPIcs.WABI.2018.4,
  author =	{Sir\'{e}n, Jouni and Garrison, Erik and Novak, Adam M. and Paten, Benedict J. and Durbin, Richard},
  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 =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.4},
  URN =		{urn:nbn:de:0030-drops-93060},
  doi =		{10.4230/LIPIcs.WABI.2018.4},
  annote =	{Keywords: FM-indexes, variation graphs, haplotypes}
}
  • Refine by Author
  • 1 Durbin, Richard
  • 1 Garrison, Erik
  • 1 Novak, Adam M.
  • 1 Paten, Benedict J.
  • 1 Sirén, Jouni

  • Refine by Classification
  • 1 Applied computing → Computational genomics
  • 1 Theory of computation → Data compression
  • 1 Theory of computation → Pattern matching

  • Refine by Keyword
  • 1 FM-indexes
  • 1 haplotypes
  • 1 variation graphs

  • Refine by Type
  • 1 document

  • Refine by Publication Year
  • 1 2018

Questions / Remarks / Feedback
X

Feedback for Dagstuhl Publishing


Thanks for your feedback!

Feedback submitted

Could not send message

Please try again later or send an E-mail