ALLPATHS 2: Small genomes assembled accurately and with high continuity from short paired reads

Genome Biology

Volumn 10, Issue 10, 2009, Pages

  MacCallum, Iain ^a   Przybylski, Dariusz ^a   Gnerre, Sante ^a   Burton, Joshua ^a   Shlyakhter, Ilya ^a   Gnirke, Andreas ^a   Malek, Joel ^b,c   McKernan, Kevin ^b   Ranade, Swati ^b,d   Shea, Terrance P ^a   Williams, Louise ^a   Young, Sarah ^a   Nusbaum, Chad ^a   Jaffe, David B ^a  

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

^b Life Technologies   (United States)

^c WEILL CORNELL MEDICAL COLLEGE   (Qatar)

^d PACIFIC BIOSCIENCES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONTIG;

ACCURACY; ARTICLE; BACTERIAL GENOME; COMPUTER PROGRAM; DNA BASE COMPOSITION; ESCHERICHIA COLI; FUNGAL GENOME; GENE SEQUENCE; GENOME SIZE; NEUROSPORA CRASSA; NONHUMAN; RHODOBACTER SPHAEROIDES; SCHIZOSACCHAROMYCES POMBE; STAPHYLOCOCCUS AUREUS; BACTERIUM; BASE PAIRING; FUNGUS; GENETICS; GENOME; GENOMICS; METHODOLOGY; REPRODUCIBILITY;

ESCHERICHIA COLI;

BACTERIA; BASE PAIRING; FUNGI; GENOME; GENOMICS; REPRODUCIBILITY OF RESULTS; SOFTWARE;

EID: 75349109607     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2009-10-10-r103     Document Type: Article

References (28)

1. Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 2005, 309:1728-1732. 10.1126/science.1117389, 16081699.
2. Service RF. Gene sequencing. The race for the $1000 genome. Science 2006, 311:1544-1546. 10.1126/science.311.5767.1544, 16543431.
3. McKernan K, Blanchard A, Kotler L, Costa G. Reagents, methods, and libraries for bead-based sequencing. Patent 2006, WO/2006/084132., http://www.wipo.int/pctdb/en/wo.jsp?wo=2006084132
4. Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavsky I, Causey M, Colonell J, Dimeo J, Efcavitch JW, Giladi E, Gill J, Healy J, Jarosz M, Lapen D, Moulton K, Quake SR, Steinmann K, Thayer E, Tyurina A, Ward R, Weiss H, Xie Z. Single-molecule DNA sequencing of a viral genome. Science 2008, 320:106-109. 10.1126/science.1150427, 18388294.
5. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk MS, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008, 456:53-59. 10.1038/nature07517, 2581791, 18987734.
6. Warren RL, Sutton GG, Jones SJ, Holt RA. Assembling millions of short DNA sequences using SSAKE. Bioinformatics 2007, 23:500-501. 10.1093/bioinformatics/btl629, 17158514.
7. Jeck WR, Reinhardt JA, Baltrus DA, Hickenbotham MT, Magrini V, Mardis ER, Dangl JL, Jones CD. Extending assembly of short DNA sequences to handle error. Bioinformatics 2007, 23:2942-2944. 10.1093/bioinformatics/btm451, 17893086.
8. Dohm JC, Lottaz C, Borodina T, Himmelbauer H. SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Res 2007, 17:1697-1706. 10.1101/gr.6435207, 2045152, 17908823.
9. Chaisson MJ, Pevzner PA. Short read fragment assembly of bacterial genomes. Genome Res 2008, 18:324-330. 10.1101/gr.7088808, 2203630, 18083777.
10. Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB. ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res 2008, 18:810-820. 10.1101/gr.7337908, 2336810, 18340039.
11. Hernandez D, Francois P, Farinelli L, Osteras M, Schrenzel J. De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res 2008, 18:802-909. 10.1101/gr.072033.107, 2336802, 18332092.
12. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008, 18:821-829. 10.1101/gr.074492.107, 2336801, 18349386.
13. Farrer RA, Kemen E, Jones JDG, Studholme DJ. De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads. FEMS Microbiol Lett 2008, 291:103-111. 10.1111/j.1574-6968.2008.01441.x, 19077061.
14. Chaisson MJ, Brinza D, Pevzner PA. De novo fragment assembly with short mate-paired reads: Does the read length matter?. Genome Res 2009, 19:336-346. 10.1101/gr.079053.108, 2652199, 19056694.
15. Broad Institute, Computational Research and Development. , http://www.broadinstitute.org/science/programs/genome-biology/crd
16. Broad Institute, Data for Short Read Assembly Paper. , ftp://ftp.broadinstitute.org/pub/papers/assembly/MacCallum2009/illumina_ data
17. Ewing B, Green P. Basecalling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998, 8:186-194.
18. Read TD, Salzberg SL, Pop M, Shumway M, Umayam L, Jiang L, Holtzapple E, Busch JD, Smith KL, Schupp JM, Solomon D, Keim P, Fraser CM. Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science 2002, 296:2028-2033. 10.1126/science.1071837, 12004073.
19. Schmutz J, Wheeler J, Grimwood J, Dickson M, Yang J, Caoile C, Bajorek E, Black S, Chan YM, Denys M, Escobar J, Flowers D, Fotopulos D, Garcia C, Gomez M, Gonzales E, Haydu L, Lopez F, Ramirez L, Retterer J, Rodriguez A, Rogers S, Salazar A, Tsai M, Myers RM. Quality assessment of the human genome sequence. Nature 2004, 429:365-368. 10.1038/nature02390, 15164052.
20. Pevzner PA, Tang H, Waterman MS. An Eulerian path approach to DNA fragment assembly. Proc Natl Acad Sci USA 2001, 98:9748-9753. 10.1073/pnas.171285098, 55524, 11504945.
21. Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ, Durbin R, Swerdlow H, Turner DJ. A large genome center's improvements to the Illumina sequencing system. Nat Methods 2008, 5:1005-1010. 10.1038/nmeth.1270, 2610436, 19034268.
22. Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M, Turner DJ. Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods 2009, 6:291-295. 10.1038/nmeth.1311, 2664327, 19287394.
23. Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, Jaffe D, FitzHugh W, Ma LJ, Smirnov S, Purcell S, Rehman B, Elkins T, Engels R, Wang S, Nielsen CB, Butler J, Endrizzi M, Qui D, Ianakiev P, Bell-Pedersen D, Nelson MA, Werner-Washburne M, Selitrennikoff CP, Kinsey JA, Braun EL, Zelter A, Schulte U, Kothe GO, Jedd G, Mewes W, et al. The genome sequence of the filamentous fungus Neurospora crassa. Nature 2003, 422:859-868. 10.1038/nature01554, 12712197.
24. Broad Institute, Science data. , http://www.broadinstitute.org/science/data
25. Nusbaum C, Ohsumi TK, Gomez J, Aquadro J, Victor TC, Warren RM, Hung DT, Birren BW, Lander ES, Jaffe DB. Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing. Nat Methods 2008, 6:67-69. 10.1038/nmeth.1286, 2613166, 19079253.
26. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437:376-380. 1464427, 16056220.
27. Applied Biosystems, SOLiD System Mate-paired Libraries Detect and Define Large Genetic Rearrangements. , http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/gen eraldocuments/cms_057555.pdf
28. Collins FS, Weissman SM. Directional cloning of DNA fragments at a large distance from an initial probe: a circularization method. Proc Natl Acad Sci USA 1984, 81:6812-6816. 10.1073/pnas.81.21.6812, 392022, 6093122.