Skip to main content

Challenge of Metagenome Assembly and Possible Standards

  • Living reference work entry
  • First Online:
Book cover Encyclopedia of Metagenomics

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Institutional subscriptions

References

  • 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.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Chain PSG, Grafham DV, et al. Genome project standards in a New Era of sequencing. Science. 2009;326(5950):236–7.

    Article  CAS  PubMed  Google Scholar 

  • Delcher AL, Phillippy A, et al. Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res. 2002;30(11):2478–83.

    Article  PubMed Central  PubMed  Google Scholar 

  • 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.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Gordon D. Viewing and editing assembled sequences using Consed. Curr Protoc Bioinforma. 2003. Chapter 11: Unit11 12.

    Google Scholar 

  • Huttenhower C, Gevers D, et al. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486(7402):207–14.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • 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.

    Article  PubMed  Google Scholar 

  • 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 

  • 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.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26(5):589–95.

    Article  PubMed Central  PubMed  Google Scholar 

  • Li H, Handsaker B, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–9.

    Article  PubMed Central  PubMed  Google Scholar 

  • 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.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Methe BA, Nelson KE, et al. A framework for human microbiome research. Nature. 2012;486(7402):215–21.

    Article  CAS  PubMed Central  Google Scholar 

  • Miller JR, Koren S, et al. Assembly algorithms for next-generation sequencing data. Genomics. 2010;95(6):315–27.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • 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 

  • Peng Y, Leung HCM, et al. Meta-IDBA: a de Novo assembler for metagenomic data. Bioinformatics. 2011;27(13):I94–101.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Schatz MC, Phillippy AM. et al. Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. Brief Bioinform. 2011.

    Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • Yilmaz P, Gilbert JA, et al. The genomic standards consortium: bringing standards to life for microbial ecology. Isme J. 2011;5(10):1565–7.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Matthew B. Scholz .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media New York

About this entry

Cite this entry

Scholz, M.B., Lo, CC., Chain, P. (2013). Challenge of Metagenome Assembly and Possible Standards. In: Nelson, K. (eds) Encyclopedia of Metagenomics. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-6418-1_26-2

Download citation

  • DOI: https://doi.org/10.1007/978-1-4614-6418-1_26-2

  • Received:

  • Accepted:

  • Published:

  • Publisher Name: Springer, New York, NY

  • Online ISBN: 978-1-4614-6418-1

  • eBook Packages: Springer Reference Biomedicine and Life SciencesReference Module Biomedical and Life Sciences

Publish with us

Policies and ethics