Data from: Viral tagging reveals discrete populations in Synechococcus viral genome sequence space

Deng L, Ignacio-Espinoza JC, Gregory AC, Poulos BT, Weitz JS, Hugenholtz P, Sullivan MB

Date Published: July 14, 2014

DOI: http://dx.doi.org/10.5061/dryad.gr3ks

 

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Title RandomizationsX1500
Downloaded 10 times
Description To estimate the variability within a population from the available metagenomic data, random candidatus genomes (CG) were generated as follows using a series of custom perl scripts. First, we recruited reads to each CG requiring at least 95% identity and a coverage of 95% of the entire length of the read. Each read was non-redundantly assigned and aligned to a CG using default parameters in MUSCLE. For each CG population, we generated 100 random CG sequences using the metagenomic data that were recruited to consensus sequences, with each base having a probability of being assigned from its relative abundance in the underlying metagenomic sequence data. Here we show the result of 1500 randomizations.
Download RandomizationsX1500.FNA (136.7 Mb)
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Title ANI_2_PCA
Downloaded 18 times
Description Matrix of ANI values as obtained from each a comparison of each candidatus genome and the reference genome. This file is used as the input to perform a PCA, which is the figure shown in the manuscript.
Download ANI_2_PCA.txt (351.3 Kb)
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Title Viral Tagged Metagenome 454
Downloaded 15 times
Description This is identical to VT_MG.fna as it appears in CAM_P_0001068 in camera.
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Title Community Metagenome
Downloaded 11 times
Description Identical to Comm_MG.fna under CAM_P_0001068.
Download Comm_MG.fna (53.83 Mb)
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Title GP23_Sequences
Downloaded 15 times
Description Gp23 Sequences amplified from the isolates, data incorporated into table 1.
Download GP23_Sequences.txt (13.47 Kb)
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Title DATA-FIGURES
Downloaded 40 times
Description Tabulated data for all the figures in the manuscript.
Download DATA-FIGURES_Replace.xls (196.0 Kb)
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Title Rarefaction files
Downloaded 36 times
Description The zip folder includes the script and tables used to generate the rarefaction curves and richness index. The tables are structured as Read, Protein, Protein Cluster
Download RAREFACTION.zip (3.473 Mb)
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Title ConsensusCGs
Downloaded 38 times
Description Assembly and gene predictions (CDS and aminoacid sequences) for the 26 candidatus genomes referred in the manuscript.
Download ConsensusCGs.zip (1.418 Mb)
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Title VT_MG_IL
Downloaded 11 times
Description Fastq sequencing data of the simplified metagenome after a Viral Tagging Experiment.
Download VT_MG_IL.fastq (3.376 Gb)
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When using this data, please cite the original publication:

Deng L, Ignacio-Espinoza JC, Gregory AC, Poulos BT, Weitz JS, Hugenholtz P, Sullivan MB (2014) Viral tagging reveals discrete populations in Synechococcus viral genome sequence space. Nature 513, 242–245. http://dx.doi.org/10.1038/nature13459

Additionally, please cite the Dryad data package:

Deng L, Ignacio-Espinoza JC, Gregory AC, Poulos BT, Weitz JS, Hugenholtz P, Sullivan MB (2014) Data from: Viral tagging reveals discrete populations in Synechococcus viral genome sequence space. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.gr3ks
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