Assisted assembly: How to improve a de novo genome assembly by using related species

Genome Biology

Volumn 10, Issue 8, 2009, Pages

  Gnerre, Sante ^a   Lander, Eric S ^a   Lindblad Toh, Kerstin ^a,b   Jaffe, David B ^a  

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^b UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANIMAL; ARTICLE; BIOLOGY; GENETICS; GENOME; HUMAN; MAMMAL; METHODOLOGY; PLASMODIUM;

ALGORITHMS; ANIMALS; COMPUTATIONAL BIOLOGY; GENOME; HUMANS; MAMMALS; PLASMODIUM;

EID: 70350012234     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2009-10-8-r88     Document Type: Article

References (17)

1. Lander ES, Waterman MS. Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics 1988, 2:231-239. 10.1016/0888-7543(88)90007-9, 3294162.
2. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, et al. Mouse Genome Sequencing Consortium Initial sequencing and analysis of the mouse genome. Nature 2002, 420:520-562. 10.1038/nature01262, 12466850, Mouse Genome Sequencing Consortium.
3. Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M, Clamp M, Chang JL, Kulbokas EJ, Zody MC, Mauceli E, Xie X, Breen M, Wayne RK, Ostrander EA, Ponting CP, Galibert F, Smith DR, DeJong PJ, Kirkness E, Alvarez P, Biagi T, Brockman W, Butler J, Chin CW, Cook A, Cuff J, Daly MJ, DeCaprio D, Gnerre S, et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 2005, 438:803-819. 10.1038/nature04338, 16341006.
4. Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, Jurka J, Kamal M, Mauceli E, Searle SM, Sharpe T, Baker ML, Batzer MA, Benos PV, Belov K, Clamp M, Cook A, Cuff J, Das R, Davidow L, Deakin JE, Fazzari MJ, Glass JL, Grabherr M, Greally JM, Gu W, et al. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 2007, 447:167-177. 10.1038/nature05805, 17495919.
5. Margulies EH, , Maduro VV, Thomas PJ, Tomkins JP, Amemiya CT, Luo M, Green D. NISC Comparative Sequencing Program Comparative sequencing provides insights about the structure and conservation of marsupial and monotreme genomes. Proc Natl Acad Sci USA 2005, 102:3354-3359. 10.1073/pnas.0408539102, 549084,549084, 15718282, NISC Comparative Sequencing Program.
6. Schwartz S, Kent W, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res 2003, 13:103-107. 10.1101/gr.809403, 430961, 12529312.
7. Pontius JU, Mullikin JC, Smith DR, , Lindblad-Toh K, Gnerre S, Clamp M, Chang J, Stephens R, Neelam B, Volfovsky N, Schäffer AA, Agarwala R, Narfström K, Murphy WJ, Giger U, Roca AL, Antunes A, Menotti-Raymond M, Yuhki N, Pecon-Slattery J, Johnson WE, Bourque G, Tesler G, , O'Brien SJ. Agencourt Sequencing Team, NISC Comparative Sequencing Program Initial sequence and comparative analysis of the cat genome. Genome Res 2007, 17:1675-1689. 10.1101/gr.6380007, 2045150, 17975172, Agencourt Sequencing Team, NISC Comparative Sequencing Program.
8. Volkman SK, Sabeti PC, DeCaprio D, Neafsey DE, Schaffner SF, Milner DA, Daily JP, Sarr O, Ndiaye D, Ndir O, Mboup S, Duraisingh MT, Lukens A, Derr A, Stange-Thomann N, Waggoner S, Onofrio R, Ziaugra L, Mauceli E, Gnerre S, Jaffe DB, Zainoun J, Wiegand RC, Birren BW, Hartl DL, Galagan JE, Lander ES, Wirth DF. A genome-wide map of diversity in Plasmodium falciparum. Nat Genet 2007, 39:113-119. 10.1038/ng1930, 17159979.
9. Broad Institute: Assisted Assembly ftp Site. , ftp://ftp.broadinstitute.org/pub/papers/comprd/assisted_assembly
10. Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, Paulsen IT, James K, Eisen JA, Rutherford K, Salzberg SL, Craig A, Kyes S, Chan MS, Nene V, Shallom SJ, Suh B, Peterson J, Angiuoli S, Pertea M, Allen J, Selengut J, Haft D, Mather MW, Vaidya AB, Martin DM, et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 2002, 419:498-511. 10.1038/nature01097, 12368864.
11. Nagarajan N, Read TD, Pop M. Scaffolding and validation of bacterial genome assemblies using optical restriction maps. Bioinformatics 2008, 24:1229-1235. 10.1093/bioinformatics/btn102, 2373919, 18356192.
12. Soderlund C, Longden I, Mott R. FPC: a system for building contigs from restriction fingerprinted clones. Comput Appl Biosci 1997, 13:523-535.
13. Sundquist A, Ronaghi M, Tang H, Pevzner P, Batzoglou S. Whole-genome sequencing and assembly with high throughput, short-read technologies. PLoS ONE 2007, 2:e484. 10.1371/journal.pone.0000484, 1871613, 17534434.
14. Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES. ARACHNE: a whole-genome shotgun assembler. Genome Res 2002, 12:177-189. 10.1101/gr.208902, 155255, 11779843.
15. Jaffe DB, Butler J, Gnerre S, Mauceli E, Lindblad-Toh K, Mesirov JP, Zody MC, Lander ES. Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res 2003, 13:91-96. 10.1101/gr.828403, 430950, 12529310.
16. Broad Institute: Computational Research and Development. , http://www.broadinstitute.org/science/programs/genome-biology/crd
17. Mammalian Genome Project: Data Release Summary. , http://www.broadinstitute.org/science/projects/mammals-models/data-release-summary