Practical evaluation of 11 de novo assemblers in metagenome assembly

Journal of Microbiological Methods

Volumn 151, Issue , 2018, Pages 99-105

  Forouzan, Esmaeil ^a   Shariati, Parvin ^a   Mousavi Maleki, Masoumeh Sadat ^a   Karkhane, Ali Asghar ^a   Yakhchali, Bagher ^a  

^a NATIONAL INSTITUTE OF GENETIC ENGINEERING AND BIOTECHNOLOGY   (Iran)

Author keywords

Assembly; Metagenome; Misassemblies; N50

Indexed keywords

ARTICLE; COMPARATIVE STUDY; COST EFFECTIVENESS ANALYSIS; GENE FUNCTION; GENE LIBRARY; GENETIC ANALYSIS; METAGENOME; NEXT GENERATION SEQUENCING; PRIORITY JOURNAL; PROCESS MODEL; QUALITY CONTROL; BIOLOGY; DNA SEQUENCE; HIGH THROUGHPUT SEQUENCING; METAGENOMICS; PROCEDURES; SOFTWARE;

COMPUTATIONAL BIOLOGY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; METAGENOME; METAGENOMICS; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 85049502928     PISSN: 01677012     EISSN: 18728359     Source Type: Journal    
DOI: 10.1016/j.mimet.2018.06.007     Document Type: Article

References (37)

1. Bankevich, A., Nurk, S., Antipov, D., Gurevich, A.A., Dvorkin, M., Kulikov, A.S., Lesin, V.M., Nikolenko, S.I., Pham, S., Prjibelski, A.D., Pyshkin, A.V., Sirotkin, A.V., Vyahhi, N., Tesler, G., Alekseyev, M.A., Pevzner, P.A., SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19 (2012), 455–477, 10.1089/cmb.2012.0021.
2. Bengtsson, M.M., Øvreås, L., Planctomycetes dominate biofilms on surfaces of the kelp Laminaria hyperborea. BMC Microbiol., 10, 2010, 261, 10.1186/1471-2180-10-261.
3. Boisvert, S., Raymond, F., Godzaridis, É., Laviolette, F., Corbeil, J., Ray Meta: scalable de novo metagenome assembly and profiling. Genome Biol., 13, 2012, R122, 10.1186/gb-2012-13-12-r122.
4. Bradnam, K.R., Fass, J.N., Alexandrov, A., Baranay, P., Bechner, M., Birol, I., Boisvert, S., Chapman, J.A., Chapuis, G., Chikhi, R., Chitsaz, H., Chou, W.-C., Corbeil, J., Del Fabbro, C., Docking, T.R., Durbin, R., Earl, D., Emrich, S., Fedotov, P., Fonseca, N.A., Ganapathy, G., Gibbs, R.A., Gnerre, S., Godzaridis, E., Goldstein, S., Haimel, M., Hall, G., Haussler, D., Hiatt, J.B., Ho, I.Y., Howard, J., Hunt, M., Jackman, S.D., Jaffe, D.B., Jarvis, E.D., Jiang, H., Kazakov, S., Kersey, P.J., Kitzman, J.O., Knight, J.R., Koren, S., Lam, T.-W., Lavenier, D., Laviolette, F., Li, Y., Li, Z., Liu, B., Liu, Y., Luo, R., Maccallum, I., Macmanes, M.D., Maillet, N., Melnikov, S., Naquin, D., Ning, Z., Otto, T.D., Paten, B., Paulo, O.S., Phillippy, A.M., Pina-Martins, F., Place, M., Przybylski, D., Qin, X., Qu, C., Ribeiro, F.J., Richards, S., Rokhsar, D.S., Ruby, J.G., Scalabrin, S., Schatz, M.C., Schwartz, D.C., Sergushichev, A., Sharpe, T., Shaw, T.I., Shendure, J., Shi, Y., Simpson, J.T., Song, H., Tsarev, F., Vezzi, F., Vicedomini, R., Vieira, B.M., Wang, J., Worley, K.C., Yin, S., Yiu, S.-M., Yuan, J., Zhang, G., Zhang, H., Zhou, S., Korf, I.F., Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience, 2, 2013, 10, 10.1186/2047-217X-2-10.
5. Chen, L., Hu, M., Huang, L., Hua, Z., Kuang, J., Li, S., Shu, W., Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage. ISME J 9 (2015), 1579–1592, 10.1038/ismej.2014.245.
6. van der Walt, A.J., van Goethem, M.W., Ramond, J.-B., Makhalanyane, T.P., Reva, O., Cowan, D.A., Assembling metagenomes, one community at a time. BMC Genomics, 18, 2017, 521, 10.1186/s12864-017-3918-9.
7. Earl, D., Bradnam, K., St John, J., Darling, A., Lin, D., Fass, J., Yu, H.O.K., Buffalo, V., Zerbino, D.R., Diekhans, M., Nguyen, N., Ariyaratne, P.N., Sung, W.-K., Ning, Z., Haimel, M., Simpson, J.T., Fonseca, N.A., Birol, İ., Docking, T.R., Ho, I.Y., Rokhsar, D.S., Chikhi, R., Lavenier, D., Chapuis, G., Naquin, D., Maillet, N., Schatz, M.C., Kelley, D.R., Phillippy, A.M., Koren, S., Yang, S.-P., Wu, W., Chou, W.-C., Srivastava, A., Shaw, T.I., Ruby, J.G., Skewes-Cox, P., Betegon, M., Dimon, M.T., Solovyev, V., Seledtsov, I., Kosarev, P., Vorobyev, D., Ramirez-Gonzalez, R., Leggett, R., Maclean, D., Xia, F., Luo, R., Li, Z., Xie, Y., Liu, B., Gnerre, S., Maccallum, I., Przybylski, D., Ribeiro, F.J., Yin, S., Sharpe, T., Hall, G., Kersey, P.J., Durbin, R., Jackman, S.D., Chapman, J.A., Huang, X., Derisi, J.L., Caccamo, M., Li, Y., Jaffe, D.B., Green, R.E., Haussler, D., Korf, I., Paten, B., Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res. 21 (2011), 2224–2241, 10.1101/gr.126599.111.
8. Forouzan, E., Maleki, M.S.M., Karkhane, A.A., Yakhchali, B., Evaluation of nine popular de novo assemblers in microbial genome assembly. J. Microbiol. Methods, 2017, 10.1016/j.mimet.2017.09.008.
9. Gans, J., Wolinsky, M., Dunbar, J., Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309 (2005), 1387–1390, 10.1126/science.1112665.
10. González-Pastor, J.E., Mirete, S., Novel metal resistance genes from microorganisms: a functional metagenomic approach. Methods Mol. Biol. 668 (2010), 273–285, 10.1007/978-1-60761-823-2_19.
11. Gurevich, A., Saveliev, V., Vyahhi, N., Tesler, G., QUAST: quality assessment tool for genome assemblies. Bioinformatics 29 (2013), 1072–1075, 10.1093/bioinformatics/btt086.
12. Hernandez, D., François, P., Farinelli, L., Østerås, M., Schrenzel, J., De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res. 18 (2008), 802–809, 10.1101/gr.072033.107.
13. Howe, A.C., Jansson, J.K., Malfatti, S.A., Tringe, S.G., Tiedje, J.M., Brown, C.T., Tackling soil diversity with the assembly of large, complex metagenomes. Proc. Natl. Acad. Sci. U. S. A. 111 (2014), 4904–4909, 10.1073/pnas.1402564111.
14. Ji, P., Zhang, Y., Wang, J., Zhao, F., MetaSort untangles metagenome assembly by reducing microbial community complexity. Nat. Commun., 8, 2017, 14306, 10.1038/ncomms14306.
15. Jia, B., Xuan, L., Cai, K., Hu, Z., Ma, L., Wei, C., NeSSM: a next-generation sequencing simulator for metagenomics. PLoS One, 8, 2013, e75448, 10.1371/journal.pone.0075448.
16. Lam, K.N., Cheng, J., Engel, K., Neufeld, J.D., Charles, T.C., Current and future resources for functional metagenomics. Front. Microbiol., 6, 2015, 10.3389/fmicb.2015.01196.
17. 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 102 (2016), 3–11, 10.1016/j.ymeth.2016.02.020.
18. Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., Yuan, J., He, G., Chen, Y., Pan, Q., Liu, Yunjie, Tang, J., Wu, G., Zhang, H., Shi, Y., Liu, Yong, Yu, C., Wang, B., Lu, Y., Han, C., Cheung, D.W., Yiu, S.-M., Peng, S., Xiaoqian, Z., Liu, G., Liao, X., Li, Y., Yang, H., Wang, Jian, Lam, T.-W., Wang, Jun, SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience, 1, 2012, 18, 10.1186/2047-217X-1-18.
19. Magoc, T., Pabinger, S., Canzar, S., Liu, X., Su, Q., Puiu, D., Tallon, L.J., Salzberg, S.L., GAGE-B: an evaluation of genome assemblers for bacterial organisms. Bioinformatics 29 (2013), 1718–1725, 10.1093/bioinformatics/btt273.
20. Mikheenko, A., Saveliev, V., Gurevich, A., MetaQUAST: evaluation of metagenome assemblies. Bioinformatics 32 (2016), 1088–1090, 10.1093/bioinformatics/btv697.
21. Miller, J.R., Koren, S., Sutton, G., Assembly algorithms for next-generation sequencing data. Genomics 95 (2010), 315–327, 10.1016/j.ygeno.2010.03.001.
22. 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., 40, 2012, e155, 10.1093/nar/gks678.
23. Nurk, S., Meleshko, D., Korobeynikov, A., Pevzner, P.A., metaSPAdes: a new versatile metagenomic assembler. Genome Res. 27 (2017), 824–834, 10.1101/gr.213959.116.
24. Olson, N.D., Treangen, T.J., Hill, C.M., 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, 10.1093/bib/bbx098.
25. Paszkiewicz, K., Studholme, D.J., De novo assembly of short sequence reads. Brief. Bioinform. 11 (2010), 457–472, 10.1093/bib/bbq020.
26. Peng, Y., Leung, H.C.M., Yiu, S.M., Chin, F.Y.L., IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28 (2012), 1420–1428, 10.1093/bioinformatics/bts174.
27. Roesch, L.F.W., Fulthorpe, R.R., Riva, A., Casella, G., Hadwin, A.K.M., Kent, A.D., Daroub, S.H., Camargo, F.A.O., Farmerie, W.G., Triplett, E.W., Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1 (2007), 283–290, 10.1038/ismej.2007.53.
28. Salzberg, S.L., Phillippy, A.M., Zimin, A., Puiu, D., Magoc, T., Koren, S., Treangen, T.J., Schatz, M.C., Delcher, A.L., Roberts, M., Marçais, G., Pop, M., Yorke, J.A., GAGE: a critical evaluation of genome assemblies and assembly algorithms. Genome Res. 22 (2012), 557–567, 10.1101/gr.131383.111.
29. Sczyrba, A., Hofmann, P., Belmann, P., Koslicki, D., Janssen, S., Dröge, J., Gregor, I., Majda, S., Fiedler, J., Dahms, E., Bremges, A., Fritz, A., Garrido-Oter, R., Jørgensen, T.S., Shapiro, N., Blood, P.D., Gurevich, A., Bai, Y., Turaev, D., Demaere, M.Z., Chikhi, R., Nagarajan, N., Quince, C., Meyer, F., Balvočiūtė M., Hansen, L.H., Sørensen, S.J., Chia, B.K.H., Denis, B., Froula, J.L., Wang, Z., Egan, R., Don Kang, D., Cook, J.J., Deltel, C., Beckstette, M., Lemaitre, C., Peterlongo, P., Rizk, G., Lavenier, D., Wu, Y.-W., Singer, S.W., Jain, C., Strous, M., Klingenberg, H., Meinicke, P., Barton, M.D., Lingner, T., Lin, H.-H., Liao, Y.-C., Silva, G.G.Z., Cuevas, D.A., Edwards, R.A., Saha, S., Piro, V.C., Renard, B.Y., Pop, M., Klenk, H.-P., Göker, M., Kyrpides, N.C., Woyke, T., Vorholt, J.A., Schulze-Lefert, P., Rubin, E.M., Darling, A.E., Rattei, T., Mchardy, A.C., Critical assessment of metagenome interpretation—a benchmark of metagenomics software. Nat. Methods 14 (2017), 1063–1071, 10.1038/nmeth.4458.
30. Simon, C., Daniel, R., Metagenomic analyses: past and future trends. Appl. Environ. Microbiol. 77 (2011), 1153–1161, 10.1128/AEM.02345-10.
31. Simpson, J.T., Durbin, R., Efficient de novo assembly of large genomes using compressed data structures. Genome Res. 22 (2012), 549–556, 10.1101/gr.126953.111.
32. Simpson, J.T., Wong, K., Jackman, S.D., Schein, J.E., Jones, S.J.M., Birol, İ., ABySS: a parallel assembler for short read sequence data. Genome Res. 19 (2009), 1117–1123, 10.1101/gr.089532.108.
33. Stefani, F.O.P., Bell, T.H., Marchand, C., de la Providencia, I.E., El Yassimi, A., St-Arnaud, M., Hijri, M., Culture-dependent and -independent methods capture different microbial community fractions in hydrocarbon-contaminated soils. PLoS One, 2015, 10, 10.1371/journal.pone.0128272.
34. Vartoukian, S.R., Palmer, R.M., Wade, W.G., Strategies for culture of “unculturable” bacteria. FEMS Microbiol. Lett. 309 (2010), 1–7, 10.1111/j.1574-6968.2010.02000.x.
35. Vollmers, J., Wiegand, S., Kaster, A.-K., Comparing and evaluating metagenome assembly tools from a Microbiologist's perspective - not only size matters!. PLoS One, 12, 2017, 10.1371/journal.pone.0169662.
36. Zerbino, D.R., Birney, E., Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18 (2008), 821–829, 10.1101/gr.074492.107.
37. Zimin, A.V., Marçais, G., Puiu, D., Roberts, M., Salzberg, S.L., Yorke, J.A., The MaSuRCA genome assembler. Bioinformatics 29 (2013), 2669–2677, 10.1093/bioinformatics/btt476.