Encyclopedia of Metagenomics

Living Edition
| Editors: Karen E. Nelson

Challenge of Metagenome Assembly and Possible Standards

Living reference work entry
DOI: https://doi.org/10.1007/978-1-4614-6418-1_26-2

Introduction

As technology and methodology have allowed for more advanced assemblies of metagenomes, the need for commensurate assignment of quality to these assemblies has become evident. There are currently no set standards for describing the quality of sequencing, assembly, or analysis of metagenomic assemblies. Uncorrected, this may lead to faulty conclusions based on assumptions that the assembly is more or less accurate, or representative of the sample, than it truly is. This need is similar to, but far more complex than, the dilemma that faced the microbial sequencing and assembly community as more and more genomes were sequenced with new technologies and assembled with novel algorithms.

For bacterial genomes, the quality of assembly and finishing efforts has been standardized for several years, resulting in a much better understanding of the types of analyses that can be performed on each level of finished genome and the resulting value. While the need for standards in...

Keywords

Recombination Rhizobium 
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References

  1. Boisvert S, Laviolette F, et al. Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. J Comput Biol. 2010;17(11):1519–33.PubMedCentralPubMedCrossRefGoogle Scholar
  2. Chain PSG, Grafham DV, et al. Genome project standards in a New Era of sequencing. Science. 2009;326(5950):236–7.PubMedCrossRefGoogle Scholar
  3. Delcher AL, Phillippy A, et al. Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res. 2002;30(11):2478–83.PubMedCentralPubMedCrossRefGoogle Scholar
  4. Godoy-Vitorino F, Goldfarb KC, et al. Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows. Isme J. 2012;6(3):531–41.PubMedCentralPubMedCrossRefGoogle Scholar
  5. Gordon D. Viewing and editing assembled sequences using Consed. Curr Protoc Bioinforma. 2003. Chapter 11: Unit11 12.Google Scholar
  6. Huttenhower C, Gevers D, et al. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486(7402):207–14.CrossRefGoogle Scholar
  7. Kant R, van Passel MWJ, et al. Genome sequence of “Pedosphaera parvula” Ellin514, an aerobic verrucomicrobial isolate from pasture soil. J Bacteriol. 2011;193(11):2900–1.PubMedCentralPubMedCrossRefGoogle Scholar
  8. Lampe JW. The human microbiome project: getting to the guts of the matter in cancer epidemiology. Cancer Epidemiol Biomarkers Prev. 2008;17(10):2523–4.PubMedCrossRefGoogle Scholar
  9. Langmead B, Trapnell C, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3).Google Scholar
  10. Leung K, Zahn H, et al. A programmable droplet-based microfluidic device applied to multiparameter analysis of single microbes and microbial communities. Proc Natl Acad Sci. 2012;109(20):7665–70.PubMedCentralPubMedCrossRefGoogle Scholar
  11. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26(5):589–95.PubMedCentralPubMedCrossRefGoogle Scholar
  12. Li H, Handsaker B, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–9.PubMedCentralPubMedCrossRefGoogle Scholar
  13. McGinnis S, Madden TL. BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res. 2004;32(Web Server issue):W20–5.PubMedCentralPubMedCrossRefGoogle Scholar
  14. Methe BA, Nelson KE, et al. A framework for human microbiome research. Nature. 2012;486(7402):215–21.PubMedCentralCrossRefGoogle Scholar
  15. Miller JR, Koren S, et al. Assembly algorithms for next-generation sequencing data. Genomics. 2010;95(6):315–27.PubMedCentralPubMedCrossRefGoogle Scholar
  16. Namiki T, Hachiya T, et al. Metavelvet: an extension of velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res. 2012.Google Scholar
  17. Peng Y, Leung HCM, et al. Meta-IDBA: a de Novo assembler for metagenomic data. Bioinformatics. 2011;27(13):I94–101.PubMedCentralPubMedCrossRefGoogle Scholar
  18. Schatz MC, Phillippy AM. et al. Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. Brief Bioinform. 2011.Google Scholar
  19. Scholz MB, Lo CC, et al. Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Curr Opin Biotechnol. 2012;23(1):9–15.PubMedCrossRefGoogle Scholar
  20. Yilmaz P, Gilbert JA, et al. The genomic standards consortium: bringing standards to life for microbial ecology. Isme J. 2011;5(10):1565–7.PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Matthew B. Scholz
    • 1
  • Chien-Chi Lo
    • 1
  • Patrick Chain
    • 2
  1. 1.Genome Science GroupLos Alamos National LaboratoryLos AlamosUSA
  2. 2.Genome Sciences, Bioscience DivisionLos Alamos National LaboratoryLos AlamosUSA