MetaSPAdes: A new versatile metagenomic assembler

Genome Research

Volumn 27, Issue 5, 2017, Pages 824-834

  Nurk, Sergey ^a   Meleshko, Dmitry ^a   Korobeynikov, Anton ^a   Pevzner, Pavel A ^a,b  

^a ST PETERSBURG STATE UNIVERSITY   (Russian Federation)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BENCHMARKING; DIPLOIDY; METAGENOME; METAGENOMICS; PRIORITY JOURNAL; STRAIN DIFFERENCE; BACTERIAL GENOME; CONTIG MAPPING; DNA SEQUENCE; GENOMICS; PROCEDURES; SOFTWARE;

CONTIG MAPPING; GENOME, BACTERIAL; GENOMICS; METAGENOME; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 85019133486     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.213959.116     Document Type: Article

References (72)

1. Antipov D, Korobeynikov A, McLean JS, Pevzner PA. 2016. hybridSPAdes: an algorithm for hybrid assembly of short and long reads. Bioinformatics 32: 1009-1015.
2. Aparicio S, Chapman J, Stupka E, Putnam N, Chia J-M, Dehal P, Christoffels A, Rash S, Hoon S, Smit A, et al. 2002. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297: 1301-1310.
3. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto J, et al. 2011. Enterotypes of the human gut microbiome. Nature 473: 1-7.
4. Ashton PM, Nair S, Dallman T, Rubino S, RabschW, Mwaigwisya S, Wain J, O'Grady J. 2014. MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island. Nat Biotechnol 33: 296-300.
5. Bankevich A, Pevzner PA. 2016. TruSPAdes: barcode assembly of TruSeq synthetic long reads. Nat Methods 13: 248-250.
6. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19: 455-477.
7. Bertin MJ, Schwartz SL, Lee J, Korobeynikov A, Dorrestein PC, Gerwick L, Gerwick WH. 2015. Spongosine production by a Vibrio harveyi strain associated with the sponge Tectitethya crypta. J Nat Prod 78: 493-499.
8. Biller SJ, Berube PM, Lindell D, Chisholm SW. 2015. Prochlorococcus: the structure and function of collective diversity. Nat Rev Microbiol 13: 13-27.
9. Boisvert S, Raymond F, Godzaridis É, Laviolette F, Corbeil J. 2012. Ray Meta: scalable de novo metagenome assembly and profiling. Genome Biol 13: R122.
10. Castelle CJ, Hug LA, Wrighton KC, Thomas BC, Williams KH, Wu D, Tringe SG, Singer SW, Eisen JA, Banfield JF. 2013. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nat Commun 4: 2120.
11. Coates RC, Podell S, Korobeynikov A, Lapidus A, Pevzner P, Sherman DH, Allen EE, Gerwick L, Gerwick WH. 2014. Characterization of cyanobacterial hydrocarbon composition and distribution of biosynthetic pathways. PLoS One 9: e851.
12. Cotten M, Oude Munnink B, Canuti M, Deijs M, Watson SJ, Kellam P, van der Hoek L. 2014. Full genome virus detection in fecal samples using sensitive nucleic acid preparation, deep sequencing, and a novel iterative sequence classification algorithm. PLoS One 9: e93269.
13. Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M, Goodstein DM, et al. 2002. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science 298: 2157-2167.
14. Dick GJ, Andersson AF, Baker BJ, Simmons SL, Thomas BC, Yelton AP, Banfield JF. 2009. Community-wide analysis of microbial genome sequence signatures. Genome Biol 10: R85.
15. Donmez N, Brudno M. 2011. Hapsembler: an assembler for highly polymorphic genomes. In Research in computational molecular biology (ed. Bafna V, Sahinalp SC), Vol. 6577, pp. 38-52. Springer, Berlin, Heidelberg.
16. Dupont CL, Rusch DB, Yooseph S, Lombardo M-J, Alexander Richter R, Valas R, Novotny M, Yee-Greenbaum J, Selengut JD, Haft DH, et al. 2012. Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. ISME J 6: 1186-1199.
17. Fu L, Niu B, Zhu Z, Wu S, LiW. 2012. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28: 3150-3152.
18. García-Löpez R, Vázquez-Castellanos JF, Moya A. 2015. Fragmentation and coverage variation in viral metagenome assemblies, and their effect in diversity calculations. Front Bioeng Biotechnol 3: 141.
19. Gevers D, Pop M, Schloss PD, Huttenhower C. 2012. Bioinformatics for the human microbiome project. PLoS Comput Biol 8: e1002779.
20. Gurevich A, Saveliev V, Vyahhi N, Tesler G. 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29: 1072-1075.
21. Haider B, Ahn T-H, Bushnell B, Chai J, Copeland A, Pan C. 2014. Omega: an overlap-graph de novo assembler for metagenomics. Bioinformatics 30: 2717-2722.
22. Hess M, Sczyrba A, Egan R, Kim T-W, Chokhawala H, Schroth G, Luo S, Clark DS, Chen F, Zhang T, et al. 2011. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331: 463-467.
23. Hug LA, Castelle CJ, Wrighton KC, Thomas BC, Sharon I, Frischkorn KR, Williams KH, Tringe SG, Banfield JF. 2013. Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling. Microbiome 1: 22.
24. The Human Microbiome Project Consortium. 2012. Structure, function and diversity of the healthy human microbiome. Nature 486: 207-214.
25. Hyatt D, Locascio PF, Hauser LJ, Uberbacher EC. 2012. Gene and translation initiation site prediction in metagenomic sequences. Bioinformatics 28: 2223-2230.
26. Iverson V, Morris RM, Frazar CD, Berthiaume CT, Morales RL, Armbrust EV. 2012. Untangling genomes from metagenomes: revealing an uncultured class of marine euryarchaeota. Science 335: 587-590.
27. Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Okuno M, Yabana M, Harada M, Nagayasu E, Maruyama H, et al. 2014. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res 24: 1384-1395.
28. Kashtan N, Roggensack SE, Rodrigue S, Thompson JW, Biller SJ, Coe A, Ding H, Marttinen P, Malmstrom RR, Stocker R, et al. 2014. Single-cell genomics reveals hundreds of coexisting subpopulations in wild prochlorococcus. Science 344: 416-420.
29. Kleigrewe K, Almaliti J, Tian IY, Kinnel RB, Korobeynikov A, Monroe EA, Duggan BM, Di Marzo V, Sherman DH, Dorrestein PC, et al. 2015. Combining mass spectrometric metabolic profiling with genomic analysis: a powerful approach for discovering natural products from cyanobacteria. J Nat Prod 78: 1671-1682.
30. Kleiner M, Hooper LV, Duerkop BA. 2015. Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes. BMC Genomics 16: 7.
31. Koren S, Treangen TJ, Pop M. 2011. Bambus 2: scaffolding metagenomes. Bioinformatics 27: 2964-2971.
32. Kuleshov V, Xie D, Chen R, Pushkarev D, Ma Z, Blauwkamp T, Kertesz M, Snyder M. 2014. Whole-genome haplotyping using long reads and statistical methods. Nat Biotechnol 32: 261-266.
33. Kuleshov V, Jiang C, Zhou W, Jahanbani F, Batzoglou S, Snyder M. 2015. Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome. Nat Biotechnol 34: 64-69.
34. Labonté JM, Swan BK, Poulos B, Luo H, Koren S, Hallam SJ, Sullivan MB, Woyke T, Wommack KE, Stepanauskas R. 2015. Single-cell genomicsbased analysis of virus-host interactions in marine surface bacterioplankton. ISME J 9: 2386-99.
35. Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357-359.
36. Laserson J, Jojic V, Koller D. 2011. Genovo: de novo assembly for metagenomes. J Comput Biol 18: 429-443.
37. Li W, Godzik A. 2006. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22: 1658-1659.
38. Li D, Liu C-M, Luo R, Sadakane K, Lam T-W. 2015. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31: 1674-1676.
39. Li D, Luo R, Liu C-M, Leung C-M, Ting H-F, Sadakane K, Yamashita H, Lam T-W. 2016. MEGAHIT v1.0: a fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods 102: 3-11.
40. Mavromatis K, Ivanova N, Barry KW, Shapiro HJ, Goltsman E, McHardy AC, Rigoutsos I, Salamov A, Korzeniewski F, Land M, et al. 2007. Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat Methods 4: 495-500.
41. McCoy RC, Taylor RW, Blauwkamp TA, Kelley JL, Kertesz M, Pushkarev D, Petrov DA, Fiston-Lavier A-S. 2014. Illumina TruSeq synthetic longreads empower de novo assembly and resolve complex, highly-repetitive transposable elements. PLoS One 9: e106689.
42. McLean JS, Lombardo M-J, Badger JH, Edlund A, Novotny M, Yee-Greenbaum J, Vyahhi N, Hall AP, Yang Y, Dupont CL, et al. 2013. Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum. Proc Natl Acad Sci 110: E2390-E2399.
43. Mende DR, Waller AS, Sunagawa S, Järvelin AI, Chan MM, Arumugam M, Raes J, Bork P. 2012. Assessment of metagenomic assembly using simulated next generation sequencing data. PLoS One 7: e31386.
44. Mikheenko A, Saveliev V, Gurevich A. 2016. MetaQUAST: evaluation of metagenome assemblies. Bioinformatics 32: 1088-1090.
45. Miller IJ, Weyna TR, Fong SS, Lim-Fong GE, Kwan JC. 2016. Single sample resolution of rare microbial dark matter in a marine invertebrate metagenome. Sci Rep 6: 34362.
46. Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, Flanigan MJ, Kravitz SA, Mobarry CM, Reinert KH, Remington KA, et al. 2000. A whole-genome assembly of Drosophila. Science 287: 2196-2204.
47. Nagarajan N, Pop M. 2013. Sequence assembly demystified. Nat Rev Genet 14: 157-67.
48. Namiki T, Hachiya T, Tanaka H, Sakakibara Y. 2012. MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res 40: e155-e155.
49. Nijkamp JF, Pop M, Reinders MJT, de Ridder D. 2013. Exploring variationaware contig graphs for (comparative) metagenomics using MaryGold. Bioinformatics 29: 2826-2834.
50. Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A, Lapidus A, Prjibelski AD, Pyshkin A, Sirotkin A, Sirotkin Y, et al. 2013. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol 20: 714-737.
51. Peng Y, Leung HCM, Yiu SM, Chin FYL. 2011. Meta-IDBA: a de novo assembler for metagenomic data. Bioinformatics 27: 94-101.
52. Peng Y, Leung HCM, Yiu SM, Chin FYL. 2012. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28: 1420-1428.
53. Pevzner PA, Tang H, Tesler G. 2004. De novo repeat classification and fragment assembly. Genome Res 14: 1786-1796.
54. Prjibelski AD, Vasilinetc I, Bankevich A, Gurevich A, Krivosheeva T, Nurk S, Pham S, Korobeynikov A, Lapidus A, Pevzner PA. 2014. ExSPAnder: a universal repeat resolver for DNA fragment assembly. Bioinformatics 30: 293-301.
55. Richter DC, Ott F, Auch AF, Schmid R, Huson DH. 2008. MetaSim: a sequencing simulator for genomics and metagenomics ed. D. Field. PLoS One 3: e3373.
56. Rosen MJ, Davison M, Bhaya D, Fisher DS. 2015. Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche. Science 348: 1019-1023.
57. Safonova Y, Bankevich A, Pevzner P. 2015. dipSPAdes: assembler for highly polymorphic diploid genomes. J Comput Biol 22: 528-545.
58. Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, et al. 2012. GAGE: a critical evaluation of genome assemblies and assembly algorithms. Genome Res 22: 557-567.
59. Shakya M, Quince C, Campbell JH, Yang ZK, Schadt CW, Podar M. 2013. Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities. Environ Microbiol 15: 1882-1899.
60. Sharon I, Kertesz M, Hug LA, Pushkarev D, Blauwkamp TA, Castelle CJ, Amirebrahimi M, Thomas BC, Burstein D, Tringe SG, et al. 2015. Accurate, multi-kb reads resolve complex populations and detect rare microorganisms. Genome Res 25: 534-543.
61. Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M. 2013. MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome Biol 14: R2.
62. Tsai Y-C, Conlan S, Deming C, Segre JA, Kong HH, Korlach J, Oh J. 2016. Resolving the complexity of human skin metagenomes using singlemolecule sequencing. MBio 7: e01948-15.
63. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. 2007. The human microbiome project. Nature 449: 804-810.
64. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF. 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37-43.
65. Vasilinetc I, Prjibelski AD, Gurevich A, Korobeynikov A, Pevzner P. 2015. Assembling short reads from jumping libraries with large insert sizes. Bioinformatics 31: 3262-3268.
66. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, NelsonW, et al. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74.
67. Vinson JP, Jaffe DB,O'Neill K, Karlsson EK, Stange-Thomann N, Anderson S, Mesirov JP, Satoh N, Satou Y, NusbaumC, et al. 2005. Assembly of polymorphic genomes: algorithms and application to Ciona savignyi. Genome Res 15: 1127-1135.
68. WuY-W, Ye Y. 2011. A novel abundance-based algorithm for binning metagenomic sequences using l-tuples. J Comput Biol 18: 523-534.
69. Wu Y-W, Tang Y-H, Tringe SG, Simmons BA, Singer SW. 2014. MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome 2: 26.
70. Xie M, Ren M, Yang C, Yi H, Li Z, Li T, Zhao J. 2016. Metagenomic analysis reveals symbiotic relationship among bacteria in microcystis-dominated community. Front Microbiol 7: 56.
71. Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W, et al. 2007. The Sorcerer II global ocean sampling expedition: expanding the universe of protein families. PLoS Biol 5: 0432-0466.
72. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821-829.