MeDuSa: A multi-draft based scaffolder

Bioinformatics

Volumn 31, Issue 15, 2015, Pages 2443-2451

  Bosi, Emanuele ^a,b   Donati, Beatrice ^b,c,d   Galardini, Marco ^e   Brunetti, Sara ^f   Sagot, Marie France ^c,d,g   Lió, Pietro ^h   Crescenzi, Pierluigi ^b   Fani, Renato ^a,b   Fondi, Marco ^a,b  

^a Department of Biology ComBo Florence Computational Biology Group   (Italy)

^b UNIVERSITY OF FLORENCE   (Italy)

^c INRIA RHÔNE ALPES   (France)

^d UNIVERSITÉ DE LYON   (France)

^e WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^f UNIVERSITY OF SIENA   (Italy)

^g UNIVERSITÉ LYON 1   (France)

^h UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; COMPUTER PROGRAM; CONTIG MAPPING; GENOMICS; PROCEDURES;

ALGORITHMS; CONTIG MAPPING; GENOMICS; SOFTWARE;

EID: 84943643130     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv171     Document Type: Article

References (26)

1. Barton, M. D. and Barton, H. A. (2012) Scaffolder - software for manual genome scaffolding. Source Code Biol. Med., 7, 4.
2. Boetzer, M. et al. (2011) Scaffolding pre-assembled contigs using sspace. Bioinformatics, 27, 578-579.
3. Cox, M. P. et al. (2010) Solexaqa: at-a-glance quality assessment of illumina second-generation sequencing data. BMC Bioinformatics, 11, 485.
4. Darling, A. E. et al. (2010) Progressivemauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One, 5, 1754-1760.
5. Dayarian, A. et al. (2010) Sopra: Scaffolding algorithm for paired reads via statistical optimization. BMC Bioinformatics, 11, 345.
6. Donmez, N. and Brudno, M. (2013) Scarpa: scaffolding reads with practical algorithms. Bioinformatics, 29, 428-434.
7. Fondi, M. et al. (2014) Draft genomes of three antarctic psychrobacter strains producing antimicrobial compounds against burkholderia cepacia complex, opportunistic human pathogens. Mar. Genomics, 13, 37-38.
8. Galardini, M. et al. (2011) Contiguator: a bacterial genomes finishing tool for structural insights on draft genomes. Source Code Biol. Med., 6, 11.
9. Gao, S. et al. (2011) Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences. J. Comput. Biol., 18, 1681-1691.
10. Gritsenko, A. A. et al. (2012) Grass: a generic algorithm for scaffolding nextgeneration sequencing assemblies. Bioinformatics, 28, 1429-1437.
11. Hunt, M. et al. (2014) A comprehensive evaluation of assembly scaffolding tools. Genome Biol., 15, R42.
12. Husemann, P. and Stoye, J. (2010) Phylogenetic comparative assembly. Algorithms Mol. Biol., 5, 3.
13. Kim, J. et al. (2013) Reference-assisted chromosome assembly. Proc. Natl. Acad. Sci. USA, 110, 1785-1790.
14. Kolmogorov, M. et al. (2014) Ragout-a reference-assisted assembly tool for bacterial genomes. Bioinformatics, 30, i302-i309.
15. Kurtz, S. et al. (2004) Versatile and open software for comparing large genomes. Genome Biol., 5, R12.
16. Langmead, B. et al. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
17. Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics, 25, 1754-1760.
18. Moran, S. et al. (1990) Approximation algorithms for covering a graph by vertex-disjoint paths of maximum total weight. Networks, 20, 55-64.
19. Rajaraman, A. et al. (2013) Fpsac: fast phylogenetic scaffolding of ancient contigs. Bioinformatics, 29, 2987-2994.
20. Reddy, T. B. et al. (2014) The genomes online database (gold) v. 5: a metadata management system based on a four level (meta) genome project classification. Nucleic Acids Res, 43, D1099-D1106.
21. Roth, A. C. et al. (2008) Algorithm of OMA for large-scale orthology inference. BMC Bioinformatics, 9, 518.
22. Salmela, L. et al. (2011) Fast scaffolding with small independent mixed integer programs. Bioinformatics, 27, 3259-3265.
23. Salzberg, S. L. et al. (2012) Gage: a critical evaluation of genome assemblies and assembly algorithms. Genome Res., 22, 557-567.
24. Silva, G. G. et al. (2013) Combining de novo and reference-guided assembly with scaffold-builder. Source Code Biol. Med., 8, 23.
25. Simpson, J. T. et al. (2009) Abyss: a parallel assembler for short read sequence data. Genome Res., 19, 1117-1123.
26. Van Hijum, S. A. et al. (2005) Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies. Nucleic Acids Res., 33(Web Server issue), W560-W566.