Biophysics and Physicobiology
Online ISSN : 2189-4779
ISSN-L : 2189-4779
Regular Article
On the use of algebraic topology concepts to check the consistency of genome assembly
Jean-François Gibrat
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JOURNALS FREE ACCESS

2019 Volume 16 Pages 444-451

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Abstract

This paper presents a preliminary work consisting of two contributions. The first one is the design of a very efficient algorithm based on an “Overlap-Layout-Consensus” (OLC) graph to assemble the long reads provided by 3rd generation technologies. The second concerns the analysis of this graph using algebraic topology concepts to determine, in advance, whether the assembly of the genome will be straightforward, i.e., whether it will lead to a pseudo-Hamiltonian path or cycle, or whether the results will need to be scrutinized. In the latter case, it will be necessary to look for “loops” in the OLC assembly graph caused by unresolved repeated genomic regions, and then try to untie the “knots” created by these regions.

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© 2019 THE BIOPHYSICAL SOCIETY OF JAPAN
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