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.
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References
Thurber RV, Haynes M, Breitbart M et al (2009) Laboratory procedures to generate viral metagenomes. Nat Protoc 4(4):470–483
Duhaime MB, Sullivan MB (2012) Ocean viruses: rigorously evaluating the metagenomic sample-to-sequence pipeline. Virology 434(2):181–186
Willner D, Hugenholtz P (2013) From deep sequencing to viral tagging: recent advances in viral metagenomics. BioEssays 35(5):436–442
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
Fancello L, Raoult D, Desnues C (2012) Computational tools for viral metagenomics and their application in clinical research. Virology 434(2):162–174
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
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
Colson P, Fancello L, Gimenez G et al (2013) Evidence of the megavirome in humans. J Clin Virol 57(3):191–200
Rampelli S, Soverini M, Turroni S et al (2016) ViromeScan: a new tool for metagenomic viral community profiling. BMC Genomics 17:165
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357–359
BMTagger (2011) ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/. Accessed 30 Aug 2012
Picard tools website. https://broadinstitute.github.io/picard/. Accessed 30 Aug 2012
The NCBI viral genome database. http://www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi?opt=virus&taxid=10239. Accessed 2 June 2015
Turnbaugh PJ, Ley RE, Hamady M et al (2007) The human microbiome project. Nature 449(7164):804–810
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
NIH Human Microbiome Project website. http://www.hmpdacc.org. Accessed 17 June 2015
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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
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DOI: https://doi.org/10.1007/978-1-4939-7683-6_14
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