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.
Article
Google Scholar
Aggarwala V, Liang G, Bushman FD. Viral communities of the human gut: metagenomic analysis of composition and dynamics. Mob DNA. 2017;8(1):12.
Article
Google Scholar
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.
Article
Google Scholar
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.
Article
CAS
Google Scholar
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.
Article
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20.
Article
CAS
Google Scholar
Breitbart M. Marine viruses: truth or dare; 2011.
Google Scholar
Darling AE, Mau B, Perna NT. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One. 2010;5(6):e11147.
Article
Google Scholar
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.
Article
Google Scholar
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.
Article
Google Scholar
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.
Article
CAS
Google Scholar
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.
Article
CAS
Google Scholar
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.
Google Scholar
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.
Article
Google Scholar
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.
Article
Google Scholar
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.
Article
CAS
Google Scholar
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.
Article
CAS
Google Scholar
Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29(8):1072–5.
Article
CAS
Google Scholar
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.
Article
CAS
Google Scholar
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.
Article
Google Scholar
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.
Article
CAS
Google Scholar
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.
Article
Google Scholar
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.
Google Scholar
Koren S, Treangen TJ, Hill CM, Pop M, Phillippy AM. Automated ensemble assembly and validation of microbial genomes. BMC bioinformatics. 2014;15(1):126.
Article
Google Scholar
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.
Article
CAS
Google Scholar
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.
Article
CAS
Google Scholar
Lin S-H, Liao Y-C. CISA: contig integrator for sequence assembly of bacterial genomes. PLoS One. 2013;8(3):e60843.
Article
CAS
Google Scholar
Lindgreen S, Adair KL, Gardner PP. An evaluation of the accuracy and speed of metagenome analysis tools. Sci Rep. 2016;6:19233.
Article
CAS
Google Scholar
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.
Article
Google Scholar
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.
Article
CAS
Google Scholar
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.
Article
CAS
Google Scholar
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet journal. 2011;17(1):10–2.
Article
Google Scholar
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.
Article
CAS
Google Scholar
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.
Article
Google Scholar
Mikheenko A, Saveliev V, Gurevich A. MetaQUAST: evaluation of metagenome assemblies. Bioinformatics. 2015;32(7):1088–90.
Article
Google Scholar
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.
Article
CAS
Google Scholar
Mirebrahim H, Close TJ, Lonardi S. De novo meta-assembly of ultra-deep sequencing data. Bioinformatics. 2015;31(12):i9–i16.
Article
CAS
Google Scholar
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.
Article
CAS
Google Scholar
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.
Article
CAS
Google Scholar
Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017;27(5):824–34.
Article
CAS
Google Scholar
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.
Paul JH. Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas? ISME J. 2008;2(6):579.
Article
CAS
Google Scholar
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.
Article
CAS
Google Scholar
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.
Article
Google Scholar
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.
Article
Google Scholar
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.
Article
Google Scholar
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.
Article
Google Scholar
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.
Article
CAS
Google Scholar
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.
Article
Google Scholar
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.
Article
CAS
Google Scholar
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.
Article
Google Scholar
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.
Article
Google Scholar
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.
Article
Google Scholar
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.
Article
Google Scholar
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.
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.
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.
Article
CAS
Google Scholar
Zerbino D, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18(5):821-9.
Article
Google Scholar