Combining de novo and reference-guided assembly with scaffold_builder

Source Code for Biology and Medicine

Volumn 8, Issue , 2013, Pages

  Silva, Genivaldo G Z ^a   Dutilh, Bas E ^b,c,d,e   Matthews, T D ^c   Elkins, Keri ^c   Schmieder, Robert ^b   Dinsdale, Elizabeth A ^c   Edwards, Robert A ^a,b,c,e,f  

^a SAN DIEGO STATE UNIVERSITY   (United States)

^b San Diego State University   (United States)

^c SAN DIEGO STATE UNIVERSITY   (United States)

^d RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^e FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^f ARGONNE NATIONAL LABORATORY   (United States)

Author keywords

De novo assembly; Genome sequencing; Next generation sequencing; Reference genome; Salmonella enterica serovar typhimurium; Salmonella typhimurium; Scaffolding

Indexed keywords

EID: 84887891404     PISSN: None     EISSN: 17510473     Source Type: Journal    
DOI: 10.1186/1751-0473-8-23     Document Type: Review

References (26)

1. Imelfort M, Edwards D. De novo sequencing of plant genomes using second-generation technologies. Brief Bioinform 2009, 10:609-618. 10.1093/bib/bbp039, 19933209.
2. Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 2011, 27:578-579. 10.1093/bioinformatics/btq683, 21149342.
3. Edwards RA, Olsen GJ, Maloy SR. Comparative genomics of closely related salmonellae. Trends Microbiol 2002, 10:94-99. 10.1016/S0966-842X(01)02293-4, 11827811.
4. Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WEG, Wetter T, Suhai S. Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res 2004, 14:1147-1159. 10.1101/gr.1917404, 419793, 15140833.
5. Pop M, Phillippy A, Delcher AL, Salzberg SL. Comparative genome assembly. Brief Bioinform 2004, 5:237-248. 10.1093/bib/5.3.237, 15383210.
6. Gnerre S, Lander ES, Lindblad-Toh K, Jaffe DB. Assisted assembly: how to improve a de novo genome assembly by using related species. Genome Biol 2009, 10:R88. 10.1186/gb-2009-10-8-r88, 2745769, 19712469.
7. Boucher Y, Cordero OX, Takemura A, Hunt DE, Schliep K, Bapteste E, Lopez P, Tarr CL, Polz MF. Local mobile gene pools rapidly cross species boundaries to create endemicity within global Vibrio cholerae populations. MBio 2011, 2:e00335-10. 3073641, 21486909.
8. Matthews TD, Edwards R, Maloy S. Chromosomal rearrangements formed by rrn recombination do not improve replichore balance in host-specific salmonella enterica serovars. PLoS ONE 2010, 5:e13503. 10.1371/journal.pone.0013503, 2957434, 20976060.
9. Matthews TD, Maloy S. Fitness effects of replichore imbalance in salmonella enterica. J Bacteriol 2010, 192:6086-6088. 10.1128/JB.00649-10, 2976461, 20870772.
10. Gao S, Sung W-K, Nagarajan N. Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences. J Comput Biol 2011, 18:1681-1691. 10.1089/cmb.2011.0170, 3216105, 21929371.
11. Barton MD, Barton HA. Scaffolder - software for manual genome scaffolding. Source Code Biol Med 2012, 7:4. 10.1186/1751-0473-7-4, 3464138, 22640820.
12. Galardini M, Biondi EG, Bazzicalupo M, Mengoni A. CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes. Source Code Biol Med 2011, 6:11. 10.1186/1751-0473-6-11, 3133546, 21693004.
13. Van Hijum SAFT, Zomer AL, Kuipers OP, Kok J. Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies. Nucleic Acids Res 2005, 33(Web Server issue):W560-W566. 1160117, 15980536.
14. Assefa S, Keane TM, Otto TD, Newbold C, Berriman M. ABACAS: algorithm-based automatic contiguation of assembled sequences. Bioinformatics 2009, 25:1968-1969. 10.1093/bioinformatics/btp347, 2712343, 19497936.
15. Vezzi F, Cattonaro F, Policriti A. e-RGA: enhanced reference guided assembly of complex genomes. EMBnet J 2011, 17:46-54.
16. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen Y-J, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim J-B, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437:376-380. 1464427, 16056220.
17. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang H-Y, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 2005, 33:5691-5702. 10.1093/nar/gki866, 1251668, 16214803.
18. McElroy KE, Luciani F, Thomas T. GemSIM: general, error-model based simulator of next-generation sequencing data. BMC Genomics 2012, 13:74. 10.1186/1471-2164-13-74, 3305602, 22336055.
19. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL. Versatile and open software for comparing large genomes. Genome Biol 2004, 5:R12. 10.1186/gb-2004-5-2-r12, 395750, 14759262.
20. Needleman SB, Wunsch CD. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 1970, 48:443-453. 10.1016/0022-2836(70)90057-4, 5420325.
21. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
22. Edwards RA, Haggerty JM, Cassman N, Busch JC, Aguinaldo K, Chinta S, Vaughn MH, Morey R, Harkins TT, Teiling C, Fredrikson K, Dinsdale EA. Microbes, metagenomes and marine mammals: enabling the next generation of scientist to enter the genomic era. BMC Genomics 2013, 14:600. 10.1186/1471-2164-14-600, 3766688, 24007365.
23. Schadt EE, Turner S, Kasarskis A. A window into third-generation sequencing. Hum Mol Genet 2010, 19:R227-R240. 10.1093/hmg/ddq416, 20858600.
24. Van Hijum SAFT, Zomer AL, Kuipers OP, Kok J. Projector: automatic contig mapping for gap closure purposes. Nucleic Acids Res 2003, 31:e144. 10.1093/nar/gng144, 275581, 14602937.
25. Helm RA, Maloy S. Rapid approach to determine rrn arrangement in salmonella serovars. Appl Environ Microbiol 2001, 67:3295-3298. 10.1128/AEM.67.7.3295-3298.2001, 93015, 11425756.
26. Darling AE, Mau B, Perna NT. ProgressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE 2010, 5:e11147. 10.1371/journal.pone.0011147, 2892488, 20593022.