Skip to main content

From Whole-Genome Shotgun Sequencing to Viral Community Profiling: The ViromeScan Tool

Part of the Methods in Molecular Biology book series (MIMB,volume 1746)

Abstract

ViromeScan is an innovative metagenomic analysis tool that allows the viral community characterization in terms of taxonomy from raw data of metagenomics sequencing. It efficiently denoises samples from reads of other microorganisms. Users can adopt the same shotgun metagenomic sequencing data to fully characterize complex microbial ecosystems, including bacteria and viruses. Here we apply ViromeScan pipeline to some examples, thus illustrating the processes computed from raw data to the final output.

Key words

  • Virome
  • Shotgun metagenomics
  • Sequencing
  • Bioinformatics
  • Pipeline

This is a preview of subscription content, access via your institution.

Buying options

Protocol
USD   49.95
Price excludes VAT (USA)
  • DOI: 10.1007/978-1-4939-7683-6_14
  • Chapter length: 5 pages
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
eBook
USD   109.00
Price excludes VAT (USA)
  • ISBN: 978-1-4939-7683-6
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
Softcover Book
USD   139.99
Price excludes VAT (USA)
Hardcover Book
USD   139.99
Price excludes VAT (USA)
Fig. 1
Fig. 2

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Thurber RV, Haynes M, Breitbart M et al (2009) Laboratory procedures to generate viral metagenomes. Nat Protoc 4(4):470–483

    CAS  CrossRef  Google Scholar 

  2. Duhaime MB, Sullivan MB (2012) Ocean viruses: rigorously evaluating the metagenomic sample-to-sequence pipeline. Virology 434(2):181–186

    CAS  CrossRef  Google Scholar 

  3. Willner D, Hugenholtz P (2013) From deep sequencing to viral tagging: recent advances in viral metagenomics. BioEssays 35(5):436–442

    CAS  CrossRef  Google Scholar 

  4. Lorenzi HA, Hoover J, Inman J et al (2011) The Viral MetaGenome Annotation Pipeline (VMGAP): an automated tool for the functional annotation of viral metagenomic shotgun sequencing data. Stand Genomic Sci 4(3):418–429

    CAS  CrossRef  Google Scholar 

  5. Fancello L, Raoult D, Desnues C (2012) Computational tools for viral metagenomics and their application in clinical research. Virology 434(2):162–174

    CAS  CrossRef  Google Scholar 

  6. Wommack KE, Bhavsar J, Polson SW et al (2012) VIROME: a standard operating procedure for analysis of viral metagenome sequences. Stand Genomic Sci 6(3):427–439

    CrossRef  Google Scholar 

  7. Roux S, Tournayre J, Mahul A et al (2014) Metavir 2: new tools for viral metagenome comparison and assembled virome analysis. BMC Bioinformatics 15:76

    CrossRef  Google Scholar 

  8. Colson P, Fancello L, Gimenez G et al (2013) Evidence of the megavirome in humans. J Clin Virol 57(3):191–200

    CAS  CrossRef  Google Scholar 

  9. Rampelli S, Soverini M, Turroni S et al (2016) ViromeScan: a new tool for metagenomic viral community profiling. BMC Genomics 17:165

    CrossRef  Google Scholar 

  10. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357–359

    CAS  CrossRef  Google Scholar 

  11. BMTagger (2011) ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/. Accessed 30 Aug 2012

  12. Picard tools website. https://broadinstitute.github.io/picard/. Accessed 30 Aug 2012

  13. The NCBI viral genome database. http://www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi?opt=virus&taxid=10239. Accessed 2 June 2015

  14. Turnbaugh PJ, Ley RE, Hamady M et al (2007) The human microbiome project. Nature 449(7164):804–810

    CAS  CrossRef  Google Scholar 

  15. TrimBWAstyle.usingBam.pl (2010) https://github.com/genome/genome/blob/master/lib/perl/Genome/Site/TGI/Hmp/HmpSraProcess/trimBWAstyle.usingBam.pl. Accessed 9 Sept 2012

  16. NIH Human Microbiome Project website. http://www.hmpdacc.org. Accessed 17 June 2015

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Simone Rampelli .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and Permissions

Copyright information

© 2018 Springer Science+Business Media, LLC

About this protocol

Verify currency and authenticity via CrossMark

Cite this protocol

Rampelli, S., Turroni, S. (2018). From Whole-Genome Shotgun Sequencing to Viral Community Profiling: The ViromeScan Tool. In: Pantaleo, V., Chiumenti, M. (eds) Viral Metagenomics. Methods in Molecular Biology, vol 1746. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7683-6_14

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7683-6_14

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7682-9

  • Online ISBN: 978-1-4939-7683-6

  • eBook Packages: Springer Protocols