1 Search Results for "Rastas, Pasi"


Document
Kermit: Guided Long Read Assembly using Coloured Overlap Graphs

Authors: Riku Walve, Pasi Rastas, and Leena Salmela

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


Abstract
With long reads getting even longer and cheaper, large scale sequencing projects can be accomplished without short reads at an affordable cost. Due to the high error rates and less mature tools, de novo assembly of long reads is still challenging and often results in a large collection of contigs. Dense linkage maps are collections of markers whose location on the genome is approximately known. Therefore they provide long range information that has the potential to greatly aid in de novo assembly. Previously linkage maps have been used to detect misassemblies and to manually order contigs. However, no fully automated tools exist to incorporate linkage maps in assembly but instead large amounts of manual labour is needed to order the contigs into chromosomes. We formulate the genome assembly problem in the presence of linkage maps and present the first method for guided genome assembly using linkage maps. Our method is based on an additional cleaning step added to the assembly. We show that it can simplify the underlying assembly graph, resulting in more contiguous assemblies and reducing the amount of misassemblies when compared to de novo assembly.

Cite as

Riku Walve, Pasi Rastas, and Leena Salmela. Kermit: Guided Long Read Assembly using Coloured Overlap Graphs. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 11:1-11:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)


Copy BibTex To Clipboard

@InProceedings{walve_et_al:LIPIcs.WABI.2018.11,
  author =	{Walve, Riku and Rastas, Pasi and Salmela, Leena},
  title =	{{Kermit: Guided Long Read Assembly using Coloured Overlap Graphs}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{11:1--11:11},
  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.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.11},
  URN =		{urn:nbn:de:0030-drops-93135},
  doi =		{10.4230/LIPIcs.WABI.2018.11},
  annote =	{Keywords: Genome assembly, Linkage maps, Coloured overlap graph}
}
  • Refine by Author
  • 1 Rastas, Pasi
  • 1 Salmela, Leena
  • 1 Walve, Riku

  • Refine by Classification
  • 1 Applied computing → Sequencing and genotyping technologies
  • 1 Mathematics of computing → Graph theory

  • Refine by Keyword
  • 1 Coloured overlap graph
  • 1 Genome assembly
  • 1 Linkage maps

  • 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