Skip to main content
SpringerLink
Log in

Workflow for Rapid Metagenome Analysis

  • Chapter
Process Design for Natural Scientists

Part of the book series: Communications in Computer and Information Science ((CCIS,volume 500))

  • 732 Accesses

Abstract

Analyses of metagenomes in life sciences present new opportunities as well as challenges to the scientific community and call for advanced computational methods and workflows. The large amount of data collected from samples via next-generation sequencing (NGS) technologies render manual approaches to sequence comparison and annotation unsuitable. Rather, fast and efficient computational pipelines are needed to provide comprehensive statistics and summaries and enable the researcher to choose appropriate tools for more specific analyses. The workflow presented here builds upon previous pipelines designed for automated clustering and annotation of raw sequence reads obtained from next-generation sequencing technologies such as 454 and Illumina. Employing specialized algorithms, the sequence reads are processed at three different levels. First, raw reads are clustered at high similarity cutoff to yield clusters which can be exported as multifasta files for further analyses. Independently, open reading frames (ORFs) are predicted from raw reads and clustered at two strictness levels to yield sets of non-redundant sequences and ORF families. Furthermore, single ORFs are annotated by performing searches against the Pfam database.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. http://weizhong-lab.ucsd.edu/cd-hit/

  2. ftp://emboss.open-bio.org/pub/EMBOSS/

  3. Blaese, L.: Data Mining for Unidentified Protein Sequences. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists. CCIS, vol. 500, pp. 73–87. Springer, Heidelberg (2014)

    Google Scholar 

  4. Ebert, B.E., Lamprecht, A.-L., Steffen, B., Blank, L.M.: Flux-P: Automating Metabolic Flux Analysis. Metabolites 2(4), 872–890 (2012)

    Article  Google Scholar 

  5. Lamprecht, A.-L.: User-Level Workflow Design. LNCS, vol. 8311. Springer, Heidelberg (2013)

    Google Scholar 

  6. Lamprecht, A.-L., Margaria, T.: Scientific Workflows and XMDD. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists. CCIS, vol. 500, pp. 1–13. Springer, Heidelberg (2014)

    Google Scholar 

  7. Lamprecht, A.-L., Margaria, T., Steffen, B.: Seven Variations of an Alignment Workflow - An Illustration of Agile Process Design and Management in Bio-jETI. In: Măndoiu, I., Wang, S.-L., Zelikovsky, A. (eds.) ISBRA 2008. LNCS (LNBI), vol. 4983, pp. 445–456. Springer, Heidelberg (2008)

    Chapter  Google Scholar 

  8. Lamprecht, A.-L., Margaria, T., Steffen, B.: Bio-jETI: A framework for semantics-based service composition. BMC Bioinformatics 10(suppl. 10), S8 (2009)

    Google Scholar 

  9. Lamprecht, A.-L., Margaria, T., Steffen, B., Sczyrba, A., Hartmeier, S., Giegerich, R.: GeneFisher-P: variations of GeneFisher as processes in Bio-jETI. BMC Bioinformatics 9 (suppl. 4), S13 (2008)

    Google Scholar 

  10. Lamprecht, A.-L., Naujokat, S., Margaria, T., Steffen, B.: Semantics-based composition of EMBOSS services. Journal of Biomedical Semantics 2(suppl. 1), S5 (2011)

    Google Scholar 

  11. Lamprecht, A.-L., Wickert, A.: The Course’s SIB Libraries. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists. CCIS, vol. 500, pp. 30–44. Springer, Heidelberg (2014)

    Google Scholar 

  12. Li, W.: Analysis and comparison of very large metagenomes with fast clustering and functional annotation. BMC Bioinformatics (2009)

    Google Scholar 

  13. Li, W., Godzik, A.: Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22(13), 1658–1659 (2006)

    Article  Google Scholar 

  14. Lis, M.: Constructing a Phylogenetic Tree. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists. CCIS, vol. 500, pp. 101–109. Springer, Heidelberg (2014)

    Google Scholar 

  15. Margaria, T., Steffen, B.: Agile IT: Thinking in User-Centric Models. In: Margaria, T., Steffen, B. (eds.) ISoLA 2008. CCIS, vol. 17, pp. 490–502. Springer, Heidelberg (2009)

    Google Scholar 

  16. Margaria, T., Steffen, B.: Business Process Modelling in the jABC: The One-Thing-Approach. In: Cardoso, J., van der Aalst, W. (eds.) Handbook of Research on Business Process Modeling. IGI Global (2009)

    Google Scholar 

  17. Margaria, T., Steffen, B.: Continuous Model-Driven Engineering. IEEE Computer 42(10), 106–109 (2009)

    Article  Google Scholar 

  18. Margaria, T., Steffen, B.: Simplicity as a Driver for Agile Innovation. Computer 43(6), 90–92 (2010)

    Article  Google Scholar 

  19. Margaria, T., Steffen, B.: Service-Orientation: Conquering Complexity with XMDD. In: Hinchey, M., Coyle, L. (eds.) Conquering Complexity, pp. 217–236. Springer, London (2012)

    Chapter  Google Scholar 

  20. Margaria, T., Steffen, B., Reitenspieß, M.: Service-Oriented Design: The Roots. In: Benatallah, B., Casati, F., Traverso, P. (eds.) ICSOC 2005. LNCS, vol. 3826, pp. 450–464. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  21. Naujokat, S., Lamprecht, A.-L., Steffen, B.: Loose Programming with PROPHETS. In: de Lara, J., Zisman, A. (eds.) Fundamental Approaches to Software Engineering. LNCS, vol. 7212, pp. 94–98. Springer, Heidelberg (2012)

    Chapter  Google Scholar 

  22. Punta, M., Coggill, P., Eberhardt, R., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J., Heger, A., Holm, L., Sonnhammer, E., Eddy, S., Bateman, A., Finn, R.: The pfam protein families database. Nucleic Acids Research (2012)

    Google Scholar 

  23. Reso, J.: Protein Classification Workflow. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists. CCIS, vol. 500, pp. 65–72. Springer, Heidelberg (2014)

    Google Scholar 

  24. Schütt, C.: Identification of Differentially Expressed Genes. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists. CCIS, vol. 500, pp. 127–139. Springer, Heidelberg (2014)

    Google Scholar 

  25. Steffen, B., Margaria, T., Nagel, R., Jörges, S., Kubczak, C.: Model-Driven Development with the jABC. In: Bin, E., Ziv, A., Ur, S. (eds.) HVC 2006. LNCS, vol. 4383, pp. 92–108. Springer, Heidelberg (2007)

    Chapter  Google Scholar 

  26. Vierheller, J.: Exploratory Data Analysis. In: Lamprecht, A.-L., Margaria, T. (eds.) Process Design for Natural Scientists. CCIS, vol. 500, pp. 110–126. Springer, Heidelberg (2014)

    Google Scholar 

  27. Wu, S., Zhu, Z., Fu, L., Niu, B., Li, W.: Webmga: A customizable web server for fast metagenomic sequence analysis (2011)

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Potsdam University, Potsdam, D-14482, Germany

    Gunnar Schulze

Authors
  1. Gunnar Schulze
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Chair Service and Software Engineering, Institute of Computer Science, University of Potsdam, Potsdam, Germany

    Anna-Lena Lamprecht

  2. Chair Software Engineering, Computer Science and Information Systems Department, University of Limerick and Lero, The Irish Software Research Center, Limerick, Ireland

    Tiziana Margaria

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Schulze, G. (2014). Workflow for Rapid Metagenome Analysis. In: Lamprecht, AL., Margaria, T. (eds) Process Design for Natural Scientists. Communications in Computer and Information Science, vol 500. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-45006-2_7

Download citation

  • DOI: https://doi.org/10.1007/978-3-662-45006-2_7

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-662-45005-5

  • Online ISBN: 978-3-662-45006-2

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation