A comprehensive evaluation of assembly scaffolding tools

Genome Biology

Volumn 15, Issue 3, 2014, Pages

  Hunt, Martin ^a   Newbold, Chris ^a,b   Berriman, Matthew ^a   Otto, Thomas D ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CONTIG;

ALGORITHM; ARTICLE; BACTERIAL GENOME; GENOME; GENOME ASSEMBLY; HUMAN; HUMAN GENOME; MACHINE LEARNING; NONHUMAN; PLASMODIUM FALCIPARUM; RHODOBACTER SPHAEROIDES; SCAFFOLDER; SEQUENCE ANALYSIS; STAPHYLOCOCCUS AUREUS; COMPARATIVE STUDY; COMPUTER PROGRAM; CONTIG MAPPING; DNA SEQUENCE; EVALUATION STUDY; GENETICS; PROCEDURES;

CONTIG MAPPING; HUMANS; PLASMODIUM FALCIPARUM; RHODOBACTER SPHAEROIDES; SEQUENCE ANALYSIS, DNA; SOFTWARE; STAPHYLOCOCCUS AUREUS;

EID: 84899091773     PISSN: None     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2014-15-3-r42     Document Type: Article

References (31)

1. Pagani I, Liolios K, Jansson J, Chen I-M, Smirnova T, Nosrat B, Markowitz VM, Kyrpides NC. The Genomes OnLine Database (GOLD) v. 4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2012, 40:D571-D579. 10.1093/nar/gkr1100, 3245063, 22135293.
2. Huson DH, Reinert K, Myers EW. The greedy path-merging algorithm for contig scaffolding. J ACM 2002, 49:603-615.
3. Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Marçais G, Pop M, Yorke JA. GAGE: a critical evaluation of genome assemblies and assembly algorithms. Genome Res 2012, 22:557-567. 10.1101/gr.131383.111, 3290791, 22147368.
4. Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HOK, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung W-K, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol I, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, et al. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res 2011, 21:2224-2241. 10.1101/gr.126599.111, 3227110, 21926179.
5. Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou W-C, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience 2013, 2:10. 10.1186/2047-217X-2-10, 3844414, 23870653.
6. Pop M, Kosack DS, Salzberg SL. Hierarchical scaffolding with Bambus. Genome Res 2004, 14:149-159. 314292, 14707177.
7. Koren S, Treangen TJ, Pop M. Bambus 2: scaffolding metagenomes. Bioinformatics 2011, 27:2964-2971. 10.1093/bioinformatics/btr520, 3198580, 21926123.
8. Gritsenko A, Nijkamp JF, Reinders MJT, de Ridder D. GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies. Bioinformatics 2012, 28:1429-1437. 10.1093/bioinformatics/bts175, 22492642.
9. Salmela L, Mäkinen V, Välimäki N, Ylinen J, Ukkonen E. Fast scaffolding with small independent mixed integer programs. Bioinformatics 2011, 27:3259-3265. 10.1093/bioinformatics/btr562, 3223363, 21998153.
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. Donmez N, Brudno M. SCARPA: scaffolding reads with practical algorithms. Bioinformatics 2013, 29:428-434. 10.1093/bioinformatics/bts716, 23274213.
12. Dayarian A, Michael TP, Sengupta AM. SOPRA: scaffolding algorithm for paired reads via statistical optimization. BMC Bioinforma 2010, 11:345.
13. 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.
14. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM, Birol I. ABySS: a parallel assembler for short read sequence data. Genome Res 2009, 19:1117-1123. 10.1101/gr.089532.108, 2694472, 19251739.
15. Simpson JT, Durbin R. Efficient de novo assembly of large genomes using compressed data structures. Genome Res 2012, 22:549-556. 10.1101/gr.126953.111, 3290790, 22156294.
16. Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu S-M, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam T-W, Wang J. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012, 1:18. 10.1186/2047-217X-1-18, 3626529, 23587118.
17. Fonseca NA, Rung J, Brazma A, Marioni JC. Tools for mapping high-throughput sequencing data. Bioinformatics 2012, 28:3169-3177. 10.1093/bioinformatics/bts605, 23060614.
18. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25:1754-1760. 10.1093/bioinformatics/btp324, 2705234, 19451168.
19. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10:R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
20. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2078-2079, 2009:25.
21. 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 M-S, Nene V, Shallom SJ, Suh B, Peterson J, Angiuoli S, Pertea M, Allen J, Selengut J, Haft D, Mather MW, Vaidya AB, Martin DMA, et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 2002, 419:498-511. 10.1038/nature01097, 3836256, 12368864.
22. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012, 9:357-359. 10.1038/nmeth.1923, 3322381, 22388286.
23. 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.
24. Burton JN, Adey A, Patwardhan RP, Qiu R, Kitzman JO, Shendure J. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat Biotechnol 2013, 31:1119-1125. 10.1038/nbt.2727, 24185095.
25. Hills M, O'Neill K, Falconer E, Brinkman R, Lansdorp PM. BAIT: Organizing genomes and mapping rearrangements in single cells. Genome Med 2013, 5:82. 10.1186/gm486, 24028793.
26. Dong Y, Xie M, Jiang Y, Xiao N, Du X, Zhang W, Tosser-Klopp G, Wang J, Yang S, Liang J, Chen W, Chen J, Zeng P, Hou Y, Bian C, Pan S, Li Y, Liu X, Wang W, Servin B, Sayre B, Zhu B, Sweeney D, Moore R, Nie W, Shen Y, Zhao R, Zhang G, Li J, Faraut T, et al. Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat Biotechnol 2013, 31:135-141.
27. Hunt M, Kikuchi T, Sanders M, Newbold C, Berriman M, Otto TD. REAPR: a universal tool for genome assembly evaluation. Genome Biol 2013, 14:R47. 10.1186/gb-2013-14-5-r47, 3798757, 23710727.
28. Otto TD, Sanders M, Berriman M, Newbold C. Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology. Bioinformatics 2010, 26:1704-1707. 10.1093/bioinformatics/btq269, 2894513, 20562415.
29. Boetzer M, Pirovano W. Toward almost closed genomes with GapFiller. Genome Biol 2012, 13:R56. 10.1186/gb-2012-13-6-r56, 3446322, 22731987.
30. Tsai IJ, Otto TD, Berriman M. Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biol 2010, 11:R41. 10.1186/gb-2010-11-4-r41, 2884544, 20388197.
31. 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.