Conference Paper

Global Optimization Approach for Circular and Chloroplast Genome Assembly

2018 International Conference on Bioinformatics and Computational Biology
Sebastien Francois, Rumen Andonov, Dominique Lavenier, Hristo Djidjev

ABSTRACT


 We describe a global optimization approach for

genome assembly where the steps of scaolding, gap-

lling, and scaold extension are simultaneously solved

in the framework of a common objective function.

The approach is based on integer programming

model for solving genome scaolding as a problem of

nding a long simple path in a specic graph that

satises additional constraints encoding the insert-size

information. The optimal solution of this problem

allows one to obtain new kind of contigs that we call

distance-based contig. We test the algorithm on a

benchmark of chloroplasts and compare the quality of

the results with recent scaolders.

BICOB 2018



ISBN:
978-1-943436-11-8
PUBLISHER:
ISCA
CHIEF EDITOR:
Waheed
CONFERENCE VENUE:
Las Vegas, NV, USA
CONTACT DETAILS:
isca-hq.org
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