| Bacterial and Virus Strains |
|
Bacteroides thetaiotaomicron VPI-5482 tdk- |
Martens, Chiang & Gordon, 2008 |
N/A |
|
B. thetaiotaomicron VPI-5482 tdk- cps1 |
Hickey et al., 2015 |
N/A |
|
B. thetaiotaomicron VPI-5482 tdk- cps2 |
Hickey et al., 2015 |
N/A |
|
B. thetaiotaomicron VPI-5482 tdk- cps3 |
Hickey et al., 2015 |
N/A |
|
B. thetaiotaomicron VPI-5482 tdk- cps4 |
Hickey et al., 2015 |
N/A |
|
B. thetaiotaomicron VPI-5482 tdk- cps5 |
Hickey et al., 2015 |
N/A |
|
B. thetaiotaomicron VPI-5482 tdk- cps6 |
Hickey et al., 2015 |
N/A |
|
B. thetaiotaomicron VPI-5482 tdk- cps7 |
Hickey et al., 2015 |
N/A |
|
B. thetaiotaomicron VPI-5482 tdk- cps8 |
Hickey et al., 2015 |
N/A |
|
B. thetaiotaomicron VPI-5482 tdk- Δcps |
Hickey et al., 2015 |
N/A |
|
Bacteroides phage ARB14 |
Porter and Hryckowian, et al. 2019 |
N/A |
|
Bacteroides phage ARB25 |
Porter and Hryckowian, et al. 2019 |
N/A |
|
Bacteroides phage DAC15 |
This study |
N/A |
|
Bacteroides phage DAC16 |
This study |
N/A |
|
Bacteroides phage DAC17 |
This study |
N/A |
|
Bacteroides phage DAC19 |
This study |
N/A |
|
Bacteroides phage DAC20 |
This study |
N/A |
|
Bacteroides phage DAC22 |
This study |
N/A |
|
Bacteroides phage DAC23 |
This study |
N/A |
|
Bacteroides phage HNL05 |
This study |
N/A |
|
Bacteroides phage HNL35 |
This study |
N/A |
|
Bacteroides phage SJC01 |
Porter and Hryckowian, et al. 2019 |
N/A |
|
Bacteroides phage SJC03 |
Porter and Hryckowian, et al. 2019 |
N/A |
|
Bacteroides phage SJC09 |
Porter and Hryckowian, et al. 2019 |
N/A |
|
Bacteroides phage SJC10 |
Porter and Hryckowian, et al. 2019 |
N/A |
|
Bacteroides phage SJC11 |
Porter and Hryckowian, et al. 2019 |
N/A |
|
Bacteroides phage SJC12 |
Porter and Hryckowian, et al. 2019 |
N/A |
|
Bacteroides phage SJC13 |
Porter and Hryckowian, et al. 2019 |
N/A |
|
Bacteroides phage SJC14 |
Porter and Hryckowian, et al. 2019 |
N/A |
|
Bacteroides phage SJC15 |
Porter and Hryckowian, et al. 2019 |
N/A |
|
Bacteroides phage SJC16 |
Porter and Hryckowian, et al. 2019 |
N/A |
|
Bacteroides phage SJC17 |
Porter and Hryckowian, et al. 2019 |
N/A |
|
Bacteroides phage SJC18 |
Porter and Hryckowian, et al. 2019 |
N/A |
|
Bacteroides phage SJC20 |
Porter and Hryckowian, et al. 2019 |
N/A |
|
Bacteroides phage SJC22 |
Porter and Hryckowian, et al. 2019 |
N/A |
|
Bacteroides phage SJC23 |
Porter and Hryckowian, et al. 2019 |
N/A |
|
Bacteroides phage SJC25 |
Porter and Hryckowian, et al. 2019 |
N/A |
| Deposited Data |
| Genomes of phage isolates |
This study |
BioProject ID PRJNA606391 |
| Genbank and fasta files of PhiSh genomes (Supplementary Data 1) |
This study |
https://purl.stanford.edu/vz665fs9726 |
| Code and data for IAP identification method (Supplementary Data 2) |
This study |
https://purl.stanford.edu/vz665fs9726 |
| Tutorial for identifying PhiSh (Supplementary Data 3) |
This study |
https://purl.stanford.edu/vz665fs9726 |
| Software and Algorithms |
| MiSeq Control Software v3.1 |
N/A |
https://support.illumina.com/sequencing/sequencing_instruments/miseq/downloads.html |
| Geneious version 9.1.5 |
N/A |
https://www.geneious.com/ |
| Bowtie2 |
Langmead and Salzberg, 2012 |
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| MetaBAT2 |
Kang et al., 2019 |
https://bitbucket.org/berkeleylab/metabat/src/master/ |
| DNA Master |
N/A |
http://cobamide2.pitt.edu/ |
| Genemark |
Besemer and Borodovsky, 2005 |
http://topaz.gatech.edu/GeneMark/license_download.cgi |
| Glimmer |
Delcher et al., 1999 |
https://sourceforge.net/projects/glimmer/ |
| tRNAscan-SE |
Lowe and Eddy, 1997 |
http://lowelab.ucsc.edu/tRNAscan-SE/ |
| vConTACT2 |
Bin Jang et al., 2019 |
https://bitbucket.org/MAVERICLab/vcontact2/downloads/ |
| Phamerator |
Cresawn et al., 2011 |
https://phamerator.org/ |
| PhageTerm |
Garneau et al., 2017 |
https://sourceforge.net/projects/phageterm/ |
| iVireons |
Seguritan et al., 2012 |
https://vdm.sdsu.edu/ivireons/download.html |
| Janus |
N/A |
http://cobamide2.pitt.edu/ |
| Splitstree |
Hudson and Bryant, 2006 |
http://www.splitstree.org/ |
| JGI IMG/VR Spacer Database |
Paez-Espino et al., 2019 |
https://img.jgi.doe.gov/vr/ |
| R version 3.4.0 |
N/A |
https://www.r-project.org/ |
| Clustal Omega |
Sievers et al., 2011 |
http://www.clustal.org/omega/ |
| The Interactive Tree of Life |
Letunic and Bork, 2019 |
https://itol.embl.de/ |
| ImageJ |
N/A |
https://imagej.nih.gov/ij/ |
| SearchSRA |
Torres et al., 2017, Levi et al., 2018, Towns et al., 2014, Stewart et al., 2015, Buchfink et al., 2015, Langmead and Salzberg, 2012) |
https://www.searchsra.org/ |
| BEDTools |
Quinlan, 2014 |
https://bedtools.readthedocs.io/en/latest/ |
| SRAdb |
Zhu et al., 2013 |
https://www.bioconductor.org/packages/release/bioc/html/SRAdb.html |
| parallel-fastq-dump 0.6.5 |
N/A |
https://github.com/rvalieris/parallel-fastq-dump |
| BBDuk |
N/A |
https://sourceforge.net/projects/bbmap/ |
| DIAMOND 0.9.24 |
Buchfink et al., 2015 |
https://bioweb.pasteur.fr/packages/pack@diamond@0.9.24 |
| Adobe Illustrator CS6 |
N/A |
https://www.adobe.com/products/illustrator.html |
| Graphpad Prism 8.4 |
N/A |
https://www.graphpad.com/scientific-software/prism/ |
