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bioinformatics:public [2014/09/29 13:02] simroux [Script packages] |
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- | ====== Tucson Marine Phage Lab's Public Script Repository ====== | ||
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- | ===== Script packages ===== | ||
- | * [[bioinformatics:scripts:toolkit|Sequence Analysis Toolkit]]\\ | ||
- | * A set of general scripts to deal with sequence file format conversion, recruitment plot or synteny plot. | ||
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- | * [[bioinformatics:scripts:popgen|Population Genomics]]\\ | ||
- | * These scripts are designed to study genetic variability within a given phage population. | ||
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- | * [[bioinformatics:scripts:sup05|Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell genomics and metagenomics]]\\ | ||
- | * This package includes the script used in [[http://elifesciences.org/content/3/e03125#sthash.sskQREWU.dpuf|Roux, S., Hawley, A.K., Torres Beltran, M., Scofield, M., Schwientek, P., Stepanauskas, R., Woyke, T., Hallam, S.J., Sullivan, M.B. (doi:10.7554/eLife.03125). Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell genomics and metagenomics]]. | ||
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- | *[[bioinformatics:scripts:Nature|Viral tagging reveals discrete populations in Synechococcus viral genome sequence space]]\\ | ||
- | * This includes the scripts used in [[http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13459.html|Deng, L., Ignacio-Espinoza, J.C., Gregory, A., Poulos, B.T., Weitz, J.S., Hugenholtz, P., Sullivan, M.B. (doi:10.1038/nature13459). Viral tagging reveals discrete populations in Synechococcus viral genome sequence space. Nature.]] | ||
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- | * [[bioinformatics:scripts:pov|The Pacific Ocean Virome (POV)]]\\ | ||
- | * This package includes the scripts used in [[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057355|Hurwitz, B.L., & Sullivan, M.B. (2013). The Pacific Ocean Virome (POV): A marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology. PLoS One. 8(2), e57355.]] | ||
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- | *[[bioinformatics:scripts:quantitative_assessment|Quantitative assessment of concentration, purification and replication in viral metagenomics]]\\ | ||
- | * This package includes the scripts used in [[http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2012.02836.x/full|Hurwitz, B.L., Deng, L., Poulos, B.T., & Sullivan, M.B. (2012). Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics. Environ Microbiol. 15(5), 1428–1440.]] | ||
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- | *[[bioinformatics:scripts:cyanophage|Phylogenomics of T4 cyanophages: Lateral gene transfer in the 'core' and origins of host genes.]]\\ | ||
- | * This includes the scripts used in [[http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2012.02704.x/abstract|Ignacio-Espinoza, J.C., & Sullivan, M.B. (2012). Phylogenomics of T4 cyanophages: Lateral gene transfer in the 'core' and origins of host genes. Environ Microbiol. 14(8), 2113-2126.]] | ||
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- | ===== Data packages ===== | ||
- | * {{:bioinformatics:scripts:taxonomy_data.zip}} | ||
- | * {{:bioinformatics:scripts:iplantsampledata.zip}} |