InteMAP: Integrated metagenomic assembly pipeline for NGS short reads

BMC Bioinformatics

Volumn 16, Issue 1, 2015, Pages

  Lai, Binbin ^a   Wang, Fumeng ^a   Wang, Xiaoqi ^a   Duan, Liping ^b   Zhu, Huaiqiu ^a  

^a PEKING UNIVERSITY   (China)

^b PEKING UNIVERSITY THIRD HOSPITAL   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DNA SEQUENCES; GENE ENCODING; GENES;

BETTER PERFORMANCE; COMPREHENSIVE ASSESSMENT; COVERAGE ESTIMATIONS; HIGH THROUGHPUT; METAGENOMIC ANALYSIS; METAGENOMIC DNA; NEXT-GENERATION SEQUENCING; RESEARCH COMMUNITIES;

PIPELINES;

ALGORITHM; DNA SEQUENCE; HIGH THROUGHPUT SEQUENCING; HUMAN; METAGENOMICS; PROCEDURES; SOFTWARE;

ALGORITHMS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; METAGENOMICS; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84938599908     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-015-0686-x     Document Type: Article

References (47)

1. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, et al. Environmental genome shotgun sequencing of Sargasso sea. Science. 2004;304:66-74.
2. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464:59-64.
3. Emmanuelle LC, Trine N, Junjin Q, Edi P, Falk H, Gwen F, et al. Richness of human gut microbiome correlates with metabolic markers. Nature. 2013;500:541-6.
4. Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, et al. A catalog of reference genomes from the human microbiome. Science. 2010;328:994-9.
5. Hu GQ, Guo JT, Liu YC, Zhu HQ. MetaTISA: Metagenomic translation initiation site annotator for improving gene start prediction. Bioinformatics. 2009;25:1843-5.
6. Zhu W, Lomsadze A, Borodovsky M. Ab initio gene identification in metagenomic sequences. Nucleic Acids Res. 2010;38, e132. doi: 10.1093/nar/gkq275 .
7. Patil KR, Haider P, Pope PB, Turnbaugh PJ, Morrison M, Scheffer T, et al. Taxonomic metagenome sequence assignment with structured output models. Nat Methods. 2011;8(3):191-2.
8. Liu YC, Guo JT, Hu GQ, Zhu HQ. Gene prediction in metagenomic fragments based on the SVM algorithm. BMC Bioinformatics. 2013;14:S12.
9. Laserson J, Jojic V, Koller D. Genovo: de novo assembly for metagenomes. J Comput Biol. 2011;18:429-43.
10. Afiahayati, Sato K, Sakakibara Y: An extended genovo metagenomic assembler by incorportating paired-end information. Peer J 2013, 1:e196.
11. Lai BB, Ding RG, Li Y, Duan LP, Zhu HQ. A de novo metagenomic assembly program for shotgun DNA reads. Bioinformatics. 2012;28:1455-62.
12. Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 2010;20:265-72.
13. Zerbino DR, Birney E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18:821-9.
14. Machelprang R, Waldrop MP, DeAngelis KM, David MM, Chavarria K, Blazewicz SJ, Rubin EM, Jansson JK: Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature 2011, 480:doi: 10.1038/nature10576 .
15. Peng Y, Leung HC, Yiu S, Chin FY. IDBA-UD: A de novo sssembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics. 2012;28(11):1420-8.
16. 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, e155.
17. Boisvert S, Raymond F, Godzaridis E, Laviolette F, Corbeil J. Ray Meta: scalable de novo metagenome assembly and profiling. Genome Biol. 2012;13(12):R122.
18. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455-77.
19. Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A, Lapidus A, et al. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol. 2013;20:714-37.
20. Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, Flanigan MJ, et al. A whole-genome assembly of Drosophila. Science. 2000;287:2896-204.
21. Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, Brownley A, et al. Aggressive assembly of pyrosequencing reads with mates. Bioinformatics. 2008;24:2818-24.
22. Haider B, Ahn TH, Bushnell B, Chai J, Copeland A, Pan C. Omega: an Overlap-graph de novo Assembler for Metagenomics. Bioinformatics. 2014;30(19):2717-22.
23. Kunin V, Copeland A, Lapidus A, Mavromatis K, Hugenholtz P. A bioinformatician's guide to metagenomics. Microbiol Mol Biol Rev. 2008;72:557-178.
24. Miller JR, Koren S, Sutton G. Assembly algorithms for next-generation sequencing data. Genomics. 2010;95:315-27.
25. Zimin AV, Smith DR, Sutton G, Yorke JA. Assembly reconciliation. Bioinformatics. 2008;24:42-5.
26. Yao G, Ye L, Gao H, Minx P, Warren WC, Weinstock GM. Graph accordance of next-generation sequence assemblies. Bioinformatics. 2012;28:13-6.
27. Vicedomini R, Vezzi F, Scalabrin S, Arvestad L, Policriti A. GAM-NGS: genomic assemblies merger for next generation sequencing. BMC Bioinformatics. 2013;14 Suppl 7:S6.
28. Scholz M, Lo CC, Chain PS. Improved assemblies using a source-agnostic pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of contigs. Sci Rep. 2014;4:6480.
29. Charuvaka A, Rangwala H. Evaluation of short read metagenomic assembly. BMC Genomics. 2011;12 Suppl 2:S8.
30. Mende DR, Waller AS, Sunagawa S, Jarvelin AI, Chan MM, Arumugam M, et al. Assessment of metagenomic assembly using simulated next generation sequencing data. PLoS One. 2012;7(2), e31386. doi: 10.1371/journal.pone.0031386 .
31. Simpson JT, Durbin R. Efficient de novo assembly of large genomes using compressed data structures. Genome Res. 2012;22(3):549-56.
32. Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, et al. MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome Biol. 2013;14:R2.
33. Kultima JR, Sunagawa S, Li J, Chen W, Chen H, Mende DR, et al. MOCAT: a metagenomics assembly and gene prediction toolkit. PLoS One. 2012;7, e47656.
34. Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, et al. GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Res. 2012;22:557-67.
35. Koren S, Treangen TJ, Pop M. Bambus 2: Scaffolding metagenomes. Bioinformatics. 2011;27:2964-71.
36. Pop M, Phillippy A, Delcher AL, Salzberg SL. Comparative genome assembly. Brief Bioinform. 2004;5:237-48.
37. Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature. 2012;490:55-60.
38. Tringe SG, Mering CV, Kobayashi A, Salamov AA, Chen K, Chang HW, et al. Comparative metagenomics of microbial mommunities. Science. 2005;308:554-7.
39. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature. 2004;428:37-43.
40. Richter DC, Ott F, Auch AF, Schmid R, Huson DH. MetaSim-a sequencing simulator for genomics and metagenomics. PLoS One. 2008;3(10), e3373.
41. Pignatelli M, Moya A. Evaluating the fidelity of de novo short read metagenomic assembly using simulated data. PLoS One. 2011;6(5), e19984.
42. Korbel JO, Abyzov A, Mu XJ, Carriero N, Cayting P, Zhang Z, et al. PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol. 2009;10:R23.
43. Mavromatis K, Ivanova N, Barry K, Shapiro H, Goltsman E, McHardy AC, et al. Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat Methods. 2007;4:495-500.
44. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, et al. Versatile and open software for comparing large genomes. Genome Biol. 2004;5:R12.
45. Phillippy AM, Schatz MC, Pop M. Genome assembly forensics: Finding the elusive mis-assembly. Genome Biol. 2008;9:R55.
46. Kelley DR, Schatz MC, Salzberg SL. Quake: Quality-aware detection and correctetion of sequencing errors. Genome Biol. 2010;11:R116.
47. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357-9.