Choice of assembly software has a critical impact on virome characterisation

Microbiome

Volumn 7, Issue 1, 2019, Pages

  Sutton, Thomas D S ^a,b   Clooney, Adam G ^a,b   Ryan, Feargal J ^a,b,c   Ross, R Paul ^a,b,d   Hill, Colin ^a,b  

^a UNIVERSITY COLLEGE CORK   (Ireland)

^b UNIVERSITY COLLEGE CORK   (Ireland)

^c SOUTH AUSTRALIAN HEALTH AND MEDICAL RESEARCH INSTITUTE   (Australia)

^d TEAGASC FOOD RESEARCH CENTRE   (Ireland)

Author keywords

Assembly; Bacteriophage; Benchmark; Comparison; Metagenome; Phage; Viral; Virome

Indexed keywords

ARTICLE; BACTERIOPHAGE; CONTROLLED STUDY; DRAWING; GASTROINTESTINAL TRACT; HUMAN; HUMAN EXPERIMENT; METAGENOME; METAGENOMICS; NONHUMAN; SIMULATION; SOFTWARE; VICUNA; CLASSIFICATION; DNA SEQUENCE; FACTUAL DATABASE; GENE LIBRARY; GENETICS; INTESTINE FLORA; ISOLATION AND PURIFICATION; VIRUS GENOME;

BACTERIOPHAGES; DATABASES, FACTUAL; GASTROINTESTINAL MICROBIOME; GENE LIBRARY; GENOME, VIRAL; HUMANS; SEQUENCE ANALYSIS, DNA;

EID: 85060649058     PISSN: None     EISSN: 20492618     Source Type: Journal    
DOI: 10.1186/s40168-019-0626-5     Document Type: Article

References (58)

1. Acuña-Amador L, Primot A, Cadieu E, Roulet A, Barloy-Hubler F. Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains. BMC Genomics. 2018;19(1):54.
2. Aggarwala V, Liang G, Bushman FD. Viral communities of the human gut: metagenomic analysis of composition and dynamics. Mob DNA. 2017;8(1):12.
3. Aguirre de Cárcer D, Angly FE, Alcamí A. Evaluation of viral genome assembly and diversity estimation in deep metagenomes. BMC Genomics. 2014;15(1):989.
4. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19(5):455-77.
5. Boisvert S, Raymond F, Godzaridis É, Laviolette F, Corbeil J. Ray Meta: scalable de novo metagenome assembly and profiling. Genome Biol. 2012;13(12):R122.
6. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114-20.
7. Breitbart M. Marine viruses: truth or dare; 2011.
8. Darling AE, Mau B, Perna NT. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One. 2010;5(6):e11147.
9. Deng X, Naccache SN, Ng T, Federman S, Li L, Chiu CY, Delwart EL. An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data. Nucleic Acids Res. 2015;43(7):e46.
10. Dutilh BE, Cassman N, McNair K, Sanchez SE, Silva GG, Boling L, Barr JJ, Speth DR, Seguritan V, Aziz RK. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat Commun. 2014;5:ncomms5498.
11. Florea L, Souvorov A, Kalbfleisch TS, Salzberg SL. Genome assembly has a major impact on gene content: a comparison of annotation in two Bos taurus assemblies. PLoS One. 2011;6(6):e21400.
12. Foulongne V, Sauvage V, Hebert C, Dereure O, Cheval J, Gouilh MA, Pariente K, Segondy M, Burguière A, Manuguerra J-C. Human skin microbiota: high diversity of DNA viruses identified on the human skin by high throughput sequencing. PLoS One. 2012;7(6):e38499.
13. Fritz A, Hofmann P, Majda S, Dahms E, Droege J, Fiedler J, Lesker TR, Belmann P, DeMaere MZ, Darling AE. CAMISIM: simulating metagenomes and microbial communities, vol. bioRxiv; 2018. p. 300970.
14. García-López R, Vázquez-Castellanos JF, Moya A. Fragmentation and coverage variation in viral metagenome assemblies, and their effect in diversity calculations. Front Bioeng Biotechnol. 2015;3:141.
15. Greenwald WW, Klitgord N, Seguritan V, Yooseph S, Venter JC, Garner C, Nelson KE, Li W. Utilization of defined microbial communities enables effective evaluation of meta-genomic assemblies. BMC Genomics. 2017;18(1):296.
16. Gritsenko AA, Nijkamp JF, Reinders MJ, Ridder D d. GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies. Bioinformatics. 2012;28(11):1429-37.
17. Guo L, Hua X, Zhang W, Yang S, Shen Q, Hu H, Li J, Liu Z, Wang X, Wang H. Viral metagenomics analysis of feces from coronary heart disease patients reveals the genetic diversity of the Microviridae. Virol Sin. 2017;32(2):130-8.
18. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29(8):1072-5.
19. Hannigan GD, Meisel JS, Tyldsley AS, Zheng Q, Hodkinson BP, SanMiguel AJ, Minot S, Bushman FD, Grice EA. The human skin double-stranded DNA virome: topographical and temporal diversity, genetic enrichment, and dynamic associations with the host microbiome. MBio. 2015;6(5):e01578-15.
20. Hesse U, van Heusden P, Kirby BM, Olonade I, van Zyl LJ, Trindade M. Virome assembly and annotation: a surprise in the Namib Desert. Front Microbiol. 2017;8:13.
21. Hurwitz BL, Sullivan MB. The Pacific Ocean Virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology. PLoS One. 2013;8(2):e57355.
22. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012;28(12):1647-9.
23. Kim K-H, Bae J-W. Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses. Appl Environ Microbiol. 2011;77:00289-11.
24. Koren S, Treangen TJ, Hill CM, Pop M, Phillippy AM. Automated ensemble assembly and validation of microbial genomes. BMC bioinformatics. 2014;15(1):126.
25. Li D, Luo R, Liu C-M, Leung C-M, Ting H-F, Sadakane K, Yamashita H, Lam T-W. MEGAHIT v1. 0: a fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods. 2016;102:3-11.
26. Lim ES, Zhou Y, Zhao G, Bauer IK, Droit L, Ndao IM, Warner BB, Tarr PI, Wang D, Holtz LR. Early life dynamics of the human gut virome and bacterial microbiome in infants. Nat Med. 2015;21(10):1228.
27. Lin S-H, Liao Y-C. CISA: contig integrator for sequence assembly of bacterial genomes. PLoS One. 2013;8(3):e60843.
28. Lindgreen S, Adair KL, Gardner PP. An evaluation of the accuracy and speed of metagenome analysis tools. Sci Rep. 2016;6:19233.
29. Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience. 2012;1(1):18.
30. Mahony J, Martel B, Tremblay DM, Neve H, Heller KJ, Moineau S, van Sinderen D. Identification of a new P335 subgroup through molecular analysis of lactococcal phages Q33 and BM13. Appl Environ Microbiol. 2013;79(14):4401-9.
31. Manrique P, Bolduc B, Walk ST, van der Oost J, de Vos WM, Young MJ. Healthy human gut phageome. Proc Natl Acad Sci. 2016;113(37):10400-5.
32. Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet journal. 2011;17(1):10-2.
33. Mavromatis K, Ivanova N, Barry K, Shapiro H, Goltsman E, McHardy AC, Rigoutsos I, Salamov A, Korzeniewski F, Land M. Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat Methods. 2007;4(6):495.
34. McCann A, Ryan FJ, Stockdale SR, Dalmasso M, Blake T, Ryan CA, Stanton C, Mills S, Ross PR, Hill C. Viromes of one year old infants reveal the impact of birth mode on microbiome diversity. PeerJ. 2018;6:e4694.
35. Mikheenko A, Saveliev V, Gurevich A. MetaQUAST: evaluation of metagenome assemblies. Bioinformatics. 2015;32(7):1088-90.
36. Minot S, Grunberg S, Wu GD, Lewis JD, Bushman FD. Hypervariable loci in the human gut virome. Proc Natl Acad Sci. 2012;109(10):3962-6.
37. Mirebrahim H, Close TJ, Lonardi S. De novo meta-assembly of ultra-deep sequencing data. Bioinformatics. 2015;31(12):i9-i16.
38. Namiki T, Hachiya T, Tanaka H, Sakakibara Y. MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res. 2012;40(20):e155.
39. Norman JM, Handley SA, Baldridge MT, Droit L, Liu CY, Keller BC, Kambal A, Monaco CL, Zhao G, Fleshner P. Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell. 2015;160(3):447-60.
40. Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017;27(5):824-34.
41. Olson ND, Treangen TJ, Hill CM, Cepeda-Espinoza V, Ghurye J, Koren S, Pop M. Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes. Brief bioinform. 2017.
42. Paul JH. Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas? ISME J. 2008;2(6):579.
43. Peng Y, Leung HC, Yiu S-M, Chin FY. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics. 2012;28(11):1420-8.
44. Roux S, Emerson JB, Eloe-Fadrosh EA, Sullivan MB. Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity. PeerJ. 2017;5:e3817.
45. Roux S, Hallam SJ, Woyke T, Sullivan MB. Viral dark matter and virus-host interactions resolved from publicly available microbial genomes. Elife. 2015;4:e08490.
46. Roux S, Solonenko NE, Dang VT, Poulos BT, Schwenck SM, Goldsmith DB, Coleman ML, Breitbart M, Sullivan MB. Towards quantitative viromics for both double-stranded and single-stranded DNA viruses. PeerJ. 2016;4:e2777.
47. Schürch AC, Schipper D, Bijl MA, Dau J, Beckmen KB, Schapendonk CM, Raj VS, Osterhaus AD, Haagmans BL, Tryland M. Metagenomic survey for viruses in Western Arctic caribou, Alaska, through iterative assembly of taxonomic units. PLoS One. 2014;9(8):e105227.
48. Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, Gregor I, Majda S, Fiedler J, Dahms E. Critical assessment of metagenome interpretation - a benchmark of metagenomics software. Nat Methods. 2017;14(11):1063.
49. Shkoporov AN, Ryan FJ, Draper LA, Forde A, Stockdale SR, Daly KM, McDonnell SA, Nolan JA, Sutton TD, Dalmasso M. Reproducible protocols for metagenomic analysis of human faecal phageomes. Microbiome. 2018;6(1):68.
50. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. ABySS: a parallel assembler for short read sequence data. Genome Res. 2009;19(6):1117-23.
51. Smits SL, Bodewes R, Ruiz-Gonzalez A, Baumgärtner W, Koopmans MP, Osterhaus AD, Schürch AC. Assembly of viral genomes from metagenomes. Front Microbiol. 2014;5:714.
52. Solden L, Lloyd K, Wrighton K. The bright side of microbial dark matter: lessons learned from the uncultivated majority. Curr Opin Microbiol. 2016;31:217-26.
53. Vázquez-Castellanos JF, García-López R, Pérez-Brocal V, Pignatelli M, Moya A. Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut. BMC Genomics. 2014;15(1):37.
54. Vollmers J, Wiegand S, Kaster A-K. Comparing and evaluating metagenome assembly tools from a microbiologist's perspective-not only size matters. PLoS One. 2017;12(1):e0169662.
55. Warwick-Dugdale J, Solonenko N, Moore K, Chittick L, Gregory AC, Allen MJ, Sullivan MB, Temperton B. Long-read metagenomics reveals cryptic and abundant marine viruses. bioRxiv. 2018.
56. White DJ, Wang J, Hall RJ. Assessing the impact of assemblers on virus detection in a de novo metagenomic analysis pipeline. J Comput Biol. 2017;24(9):874-881.
57. Yang X, Charlebois P, Gnerre S, Coole MG, Lennon NJ, Levin JZ, Qu J, Ryan EM, Zody MC, Henn MR. De novo assembly of highly diverse viral populations. BMC Genomics. 2012;13(1):475.
58. Zerbino D, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18(5):821-9.