Computational Mathematics

Parallel merging method to integrate different genome assemblies

K. V. Romanenkov^a, A. N. Salnikov^a, A. V. Alexeevski<sup>b

a</sup> Lomonosov Moscow State University, Moscow, Russian Federation
^b A.N. Belozersky Institute Of Physico-Chemical Biology, Moscow, Russian Federation

Abstract: In this paper research in the field of application multiprocessor systems for genome assemblies reconciliation has been carried out. A large number of algorithmic approaches aimed to solve the task of de novo assembly from short reads, however the results of their work on the same raw data often differ essentially. Due to the large data volume the computations in the distributed memory model on computational cluster are required. Authors develop merging algorithm to integrate different genome assemblies based on distributed weighted contig graph. The proposed method integrates a combination of draft assemblies reducing resulting contigs fragmentation. Sequential version of the algorithm is implemented in C/C++ and is available at https://bitbucket.org/kromanenkov/gar/.

Keywords: bioinformatics, multiprocessor systems, parallel algorithms.

UDC: 004.942

Received: 17.08.2015

DOI: 10.14529/cmse160103

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