| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Deposited Data | ||
| Aiemjoy et al., 2019 sequencing reads | Aiemjoy et al., 2019 | NCBI Sequence Read Archive (SRA) - see Table S1 for details |
| Broecker et al., 2016 sequencing reads | Broecker et al., 2016 | NCBI Sequence Read Archive (SRA) - see Table S1 for details |
| Chehoud et al., 2016 sequencing reads | Chehoud et al., 2016 | NCBI Sequence Read Archive (SRA) - see Table S1 for details |
| Clooney et al., 2019 sequencing reads | Clooney et al., 2019 | NCBI Sequence Read Archive (SRA) - PRJNA552463 |
| Draper et al., 2018 sequencing reads | Draper et al., 2018 | NCBI Sequence Read Archive (SRA) - see Table S1 for details |
| Fernandes et al., 2019 sequencing reads | Fernandes et al., 2019 | NCBI Sequence Read Archive (SRA) - see Table S1 for details |
| Giloteaux et al., 2016 sequencing reads | Giloteaux et al., 2016 | MG-RAST - see Table S1 for details |
| Han et al., 2018 sequencing reads | Han et al., 2018 (originally from Li et al., 2017) | NCBI Sequence Read Archive (SRA) - see Table S1 for details |
| Kang et al., 2017 sequencing reads | Kang et al., 2017 | iVirus - see Table S1 for details |
| Kramná et al., 2015 sequencing reads | Kramná et al., 2015 | NCBI Sequence Read Archive (SRA) - see Table S1 for details |
| Lim et al., 2015 sequencing reads | Lim et al., 2015 | NCBI Sequence Read Archive (SRA) - see Table S1 for details |
| Ly et al., 2016 sequencing reads | Ly et al., 2016 | NCBI Sequence Read Archive (SRA) - see Table S1 for details |
| Ma et al., 2019 sequencing reads | Ma et al., 2018 | NCBI Sequence Read Archive (SRA) - see Table S1 for details |
| Manrique et al., 2016 sequencing reads | Manrique et al., 2016 | NCBI Sequence Read Archive (SRA) - see Table S1 for details |
| McCann et al., 2018 sequencing reads | McCann et al., 2018 | NCBI Sequence Read Archive (SRA) - see Table S1 for details |
| Minot et al., 2011 sequencing reads | Minot et al., 2011 | NCBI Sequence Read Archive (SRA) - see Table S1 for details |
| Minot et al., 2012 sequencing reads | Minot et al., 2012 | NCBI Sequence Read Archive (SRA) - see Table S1 for details |
| Minot et al., 2013 sequencing reads | Minot et al., 2013 | NCBI Sequence Read Archive (SRA) - see Table S1 for details |
| Monaco et al., 2016 sequencing reads | Monaco et al., 2016 | NCBI Sequence Read Archive (SRA) - see Table S1 for details |
| Moreno-Gallego et al., 2019 sequencing reads | Moreno-Gallego et al., 2019 | European Nucleotide Archive (ENA) - see Table S1 for details |
| Neto et al. (unpublished) sequencing reads | Unpublished data | iVirus -- we were given some of the reads before publication |
| Norman et al., 2015 sequencing reads | Norman et al., 2015 | NCBI Sequence Read Archive (SRA) - see Table S1 for details |
| Pérez-Brocal et al., 2013 sequencing reads | Pérez-Brocal et al., 2013 | NCBI Sequence Read Archive (SRA) - see Table S1 for details |
| Rampelli et al., 2017 sequencing reads | Rampelli et al., 2017 | NCBI Sequence Read Archive (SRA) - see Table S1 for details |
| Reyes et al., 2010 sequencing reads | Reyes et al., 2010 | NCBI Sequence Read Archive (SRA) - see Table S1 for details |
| Reyes et al., 2015 sequencing reads | Reyes et al., 2015 | NCBI Sequence Read Archive (SRA) - see Table S1 for details |
| Shkoporov et al., 2018 sequencing reads | Shkoporov et al., 2018 | NCBI Sequence Read Archive (SRA) - see Table S1 for details |
| Shkoporov et al., 2019 sequencing reads | Shkoporov et al., 2019 | NCBI Sequence Read Archive (SRA) - see Table S1 for details |
| Stockdale et al., 2018 sequencing reads | Stockdale et al., 2018 | NCBI Sequence Read Archive (SRA) - see Table S1 for details |
| Yinda et al., 2019 sequencing reads | Yinda et al., 2019 | NCBI Sequence Read Archive (SRA) - see Table S1 for details |
| Zhao et al., 2017 sequencing reads | Zhao et al., 2017 | NCBI Sequence Read Archive (SRA) - see Table S1 for details |
| Zuo et al., 2018 sequencing reads | Zuo et al., 2018 | NCBI Sequence Read Archive (SRA) - see Table S1 for details |
| Zuo et al., 2019 sequencing reads | Zuo et al., 2019 | NCBI Sequence Read Archive (SRA) - see Table S1 for details |
| Software and Algorithms | ||
| nucmer (MUMmer3.23) | Kurtz et al., 2004 | https://sourceforge.net/projects/mummer/ |
| bbmap 37.57 | https://jgi.doe.gov/data-and-tools/bbtools/ | https://jgi.doe.gov/data-and-tools/bbtools/ |
| metaSPAdes 3.11 | Nurk et al., 2017 | https://github.com/ablab/spades/releases |
| prodigal 2.6.1 | Hyatt et al., 2010 | https://github.com/hyattpd/Prodigal |
| diamond | Buchfink et al., 2014 | https://github.com/bbuchfink/diamond |
| VirSorter v2 | Roux et al., 2015 | https://github.com/simroux/VirSorter |
| VirFinder | Ren et al., 2017 | https://github.com/jessieren/VirFinder |
| CAT | Cambuy et al., 2016 | https://github.com/dutilh/CAT |
| BUSCO | Simão et al., 2015 | https://busco.ezlab.org/ |
| Viral protein families (VPFs) | Paez-Espino et al., 2017 | http://portal.nersc.gov/dna/microbial/prokpubs/EarthVirome_DP/final_list.hmms |
| hmmmr | Finn et al., 2015 | http://www.hmmer.org/ |
| blast 2.4.0+ | ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/ | ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/ |
| IMG/VR v4 | Paez-Espino et al., 2017 | https://img.jgi.doe.gov/cgi-bin/vr/main.cgi |
| Viral Refseq v96 | https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/ | https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/ |
| vConTACT2 | Bin Jang et al., 2019 | https://bitbucket.org/MAVERICLab/vcontact2 |
| minced | Bland et al., 2007 | https://github.com/ctSkennerton/minced |
| tRNA-scan | Lowe and Eddy, 1997 | http://lowelab.ucsc.edu/tRNAscan-SE/ |
| MArVD | Vik et al., 2017 | https://bitbucket.org/MAVERICLab/marvd |
| WIsH | Galiez et al., 2017 | https://github.com/soedinglab/WIsH |
| MCL | Enright et al., 2002 | https://micans.org/mcl/ |
| bowtie2 | Langmead and Salzberg, 2012 | https://github.com/BenLangmead/bowtie2 |
| coverM | https://github.com/wwood/CoverM | https://github.com/wwood/CoverM |
| bedtools | Quinlan and Hall, 2010 | https://github.com/arq5x/bedtools2 |
| GTDB-Tk v1.1 | Parks et al., 2020 | https://github.com/Ecogenomics/GTDBTk |
| vegan (R package) | Dixon, 2003 | https://cran.r-project.org/web/packages/vegan/index.html |
| maps (R package) | https://cran.r-project.org/web/packages/maps/index.html | https://cran.r-project.org/web/packages/maps/index.html |
| pheatmap (R package) | https://cran.r-project.org/web/packages/pheatmap/index.html | https://cran.r-project.org/web/packages/pheatmap/index.html |
| SpiecEasi (R package) | https://www.rdocumentation.org/packages/SpiecEasi/versions/0.1.4 | https://www.rdocumentation.org/packages/SpiecEasi/versions/0.1.4 |
| igragh (R package) | https://cran.r-project.org/web/packages/igraph/ | https://cran.r-project.org/web/packages/igraph/ |
| ggplot2 (R package) | https://cran.r-project.org/web/packages/ggplot2/index.html | https://cran.r-project.org/web/packages/ggplot2/index.html |
| ggpubr (R package) | https://cran.r-project.org/web/packages/ggpubr/index.html | https://cran.r-project.org/web/packages/ggpubr/index.html |
| gtools (R package) | https://cran.r-project.org/web/packages/gtools/index.html | https://cran.r-project.org/web/packages/gtools/index.html |
| biomod2 (R package) | https://cran.r-project.org/web/packages/biomod2/index.html | https://cran.r-project.org/web/packages/biomod2/index.html |
| BiodiveristyR (R package) | https://cran.r-project.org/web/packages/BiodiversityR/index.html | https://cran.r-project.org/web/packages/BiodiversityR/index.html |
| Analyses scripts and input data (per Figure) | This paper | https://bitbucket.org/MAVERICLab/GVD |
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