Geodesic
Parallel merging method to integrate different genome assemblies
Vestnik Ûžno-Uralʹskogo gosudarstvennogo universiteta. Seriâ Vyčislitelʹnaâ matematika i informatika, Tome 5 (2016) no. 1, pp. 24-34 Cet article a éte moissonné depuis la source Math-Net.Ru

Voir la notice de l'article

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. 
@article{VYURV_2016_5_1_a2,
     author = {K. V. Romanenkov and A. N. Salnikov and A. V. Alexeevski},
     title = {Parallel merging method to integrate different genome assemblies},
     journal = {Vestnik \^U\v{z}no-Uralʹskogo gosudarstvennogo universiteta. Seri\^a Vy\v{c}islitelʹna\^a matematika i informatika},
     pages = {24--34},
     year = {2016},
     volume = {5},
     number = {1},
     language = {ru},
     url = {http://geodesic.mathdoc.fr/item/VYURV_2016_5_1_a2/}
}
TY  - JOUR
AU  - K. V. Romanenkov
AU  - A. N. Salnikov
AU  - A. V. Alexeevski
TI  - Parallel merging method to integrate different genome assemblies
JO  - Vestnik Ûžno-Uralʹskogo gosudarstvennogo universiteta. Seriâ Vyčislitelʹnaâ matematika i informatika
PY  - 2016
SP  - 24
EP  - 34
VL  - 5
IS  - 1
UR  - http://geodesic.mathdoc.fr/item/VYURV_2016_5_1_a2/
LA  - ru
ID  - VYURV_2016_5_1_a2
ER  - 
%0 Journal Article
%A K. V. Romanenkov
%A A. N. Salnikov
%A A. V. Alexeevski
%T Parallel merging method to integrate different genome assemblies
%J Vestnik Ûžno-Uralʹskogo gosudarstvennogo universiteta. Seriâ Vyčislitelʹnaâ matematika i informatika
%D 2016
%P 24-34
%V 5
%N 1
%U http://geodesic.mathdoc.fr/item/VYURV_2016_5_1_a2/
%G ru
%F VYURV_2016_5_1_a2
K. V. Romanenkov; A. N. Salnikov; A. V. Alexeevski. Parallel merging method to integrate different genome assemblies. Vestnik Ûžno-Uralʹskogo gosudarstvennogo universiteta. Seriâ Vyčislitelʹnaâ matematika i informatika, Tome 5 (2016) no. 1, pp. 24-34. http://geodesic.mathdoc.fr/item/VYURV_2016_5_1_a2/

[1] J.R. Miller, S. Koren, G. Sutton, “Assembly Algorithms for Next-Generation Sequencing Data”, Genomics, 95:6 (2010), 315–327 | DOI

[2] NCBI, BD Assembly, genom cheloveka, (data obrascheniya: 1.08.2015) http://www.ncbi.nlm.nih.gov/assembly/883148

[3] Metainformatsiya o genomakh eukariotov na saite NCBI, (data obrascheniya: 1.08.2015) ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/eukaryotes.txt

[4] R. Vicedomini, F. Vezzi, S. Scalabrin, L. Arvestad, A. Policriti, “Gam-Ngs: Genomic Assemblies Merger for Next Generation Sequencing”, BMC Bioinformatics, 14(Suppl.7):1 (2013), 1–18 | DOI

[5] G. Yao, L. Ye, H. Gao, P. Min, W.C. Warren, G.M. Weinstock, “Graph Accordance of Nextgeneration Sequence Assemblies”, Bioinformatics, 28:1 (2012), 13–16 | DOI

[6] A.V. Zimin, D.R. Smith, G. Sutton, J.A. Yorke, “Assembly Reconciliation”, Bioinformatics, 24:1 (2008), 42–45 | DOI

[7] Zorro – the Masked Assembler, (data obrascheniya: 22.07.2015) http://lge.ibi.unicamp.br/zorro/

[8] European Nucleotide Archive, (data obrascheniya: 1.08.2015) http://www.ebi.ac.uk/ena/data/view/SRR122309

[9] Encephalitozoon Cuniculi GB-M1, (data obrascheniya: 1.08.2015) http://www.ncbi.nlm.nih.gov/genome/39?genomeȧssemblyi̇d=22671

[10] A. Gurevich, V. Saveliev, N. Vyahhi, G. Tesler, “Quast: Quality Assessment Tool for Genome Assemblies”, Bioinformatics, 29:8 (2013), 1072–1075 | DOI

[11] S. Koren, T.J. Treangen, C.M. Hill, M. Pop, A.M. Phillippy, “Automated Ensemble Assembly and Validation of Microbial Genomes”, BMC Bioinformatics, 15:5 (2014), 126–134 | DOI

[12] J.T. Simpson, R. Durbin, “Efficient Construction of an Assembly String Graph Using the FM-Index”, Bioinformatics, 26:12 (2010), 367–373 | DOI